Home   |  About Startbioinfo | Other web-portals 

Categories of resources

Suggested Readings
 
 
Total resources - 73
A compilation and categorization of next-generation sequencing resources : SNP discovery
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
ANNOVAR
http://www.openbioinformatics.org/annovar/
1. ANNOVAR annotate genetic variants detected from diverse genomes including human genome hg18/ hg19, as well as mouse, worm, fly, yeast and many other organisms. 2. It can perform Gene-based, region-based and filter-based annotations.
Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high throughput sequencing data. Nucleic Acids Res. 2010 Sep;38(16):e164. Epub 2010 Jul 3. PMID:20601685.
2010
50
Avadis NGS
http://www.avadis-ngs.com/
1. It is used for data analysis, visualization, and management of data generated by next-generation sequencing (NGS) platforms. 2. It has the following features integrated with the software: a) Genome browser (visualize sequenced reads on complete genome). b) Variant support view (which lists the SNPs and small InDels that were detected during SNP analysis). c) Pathway analysis (how genes interact with each other). d) Alternative splicing analysis e) SNP detection f) BIOBASE genome Trax (can be accessed within Avadis NGS).
Not available
Not available
96
Free trial version is available for 20 days.
ACCUSA
ftp://bbc.mdc-berlin.de/software
1. It is an accurate SNP caller for next generation sequencing data. 2. It can detect SNPs by considering both read and reference genome's quality scores. 3. It uses an Bayesian framework algorithm.
Fröhler S, Dieterich C. ACCUSA-accurate SNP calling on draft genomes.Bioinformatics. 2010 May 15;26(10):1364-5. Epub 2010 Apr 1. PMID: 20363730.
2010
100
Alcovna - Algorithms for Comparing and Vizualizing Non Assembled data
http://alcovna.genouest.org/
1. Used for SNP discovery. 2. Compares and visualize non assembled data. 3. Validate an assembly based on de-Bruijn graph.
Not available
Not available
100
Atlas-SNP2
http://www.hgsc.bcm.tmc.edu/cascade-tech-software_atlas_snp-ti.hgsc
1. Used for SNP discovery. 2. Supports data from roche 454 and illumina platform. 3. It also needs installation of SAMtools.
Shen Y, Wan Z, Coarfa C, Drabek R, Chen L, Ostrowski EA, Liu Y, Weinstock GM, Wheeler DA, Gibbs RA, Yu F. A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res. 2010 Feb;20(2):273-80. Epub 2009 Dec 17. PubMed PMID: 20019143; PubMed Central PMCID: PMC2813483.
2010
100
Requires installation of SAMTools in the path.
AVA - Amplicon Variant Analyzer
http://my454.com/products/analysis-software/index.asp
1. Lacks advanced coverage analysis. 2. Data is not stored in a structured way (i.e. flat files instead of storage in a database).
Not available
Not available
100
Request has to be sent for the free download of the software.
Bambino
https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html
1. Capable of pooling data from multiple source files. 2. It has graphical viewer and SNP/indel detector. 3. Displays mappings of dbSNP SNP sites and reference protein sequences, using UCSC genome annotations. 4. Calculates protein coding changes caused by SNPs in NCBI RefSeqs.
Edmonson MN, Zhang J, Yan C, Finney RP, Meerzaman DM, Buetow KH. Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format. Bioinformatics. 2011 Mar 15;27(6):865-6. Epub 2011 Jan 28. PubMed PMID: 21278191; PubMed Central PMCID: PMC3051333.
2011
100
CLCbio Genomics
http://www.clcbio.com/index.php?id=1243
1. Analyse genomic, transcriptomic, and epigenomic data. It is a command-line program. 2. Supports de novo assembly of paired-end data and hybrid assembly of multiple data types. 3. Handles short and long read assembly, as well as gapped and ungapped alignment.
Not available
Not available
100
CloudBurst
http://sourceforge.net/apps/mediawiki/cloudburst-bio/index.php?title=CloudBurst
1. CloudBurst is a new parallel read-mapping algorithm optimized for mapping sequence data to the human genome and other reference genomes, for use in a variety of biological analysis including SNP discovery, genotyping, and personal genomics. 2. CloudBurst's running time scales linearly with the number of reads mapped, and with near linear speed-up as the number of processors increases. 3. By using 24 core processor or large cloud compute 96 cores configured systems, it can reduce the running time of mapping human genomes. 4. it is as open-sourcesoftware, serves as a model for parallelizing other bioinformatics algorithms with MapReduce.
Schatz MC. CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics. 2009 Jun 1;25(11):1363-9. Epub 2009 Apr 8. PMID: 19357099
2009
100
CoNAn-SNV
http://compbio.bccrc.ca/?page_id=342
1. Used for SNP discovery in whole genome sequencing data. 2. Has information about copy number state of different genomic segments into the inference of single nucleotide variants.
Not available
Not available
100
Corona-Lite
http://solidsoftwaretools.com/gf/project/corona/
1. Use with large genomes such as Human, Mouse, A. thaliana and C. elegans. 2. Mapping SOLiD reads to reference genomes, pairing for mate-pair runs, SNP calling and generating consensus sequences.
Not available
Not available
100
URL is not working and a message "This webpage will be removed on May 15, 2012" is seen, as on 9th May 2012.
CRISP
http://www.stsiweb.org/index.php/infrastructure/software_data/variant_detection_for_pooled_sequence_data_crisp/
1. It is used for the identification of Single Nucleotide Polymorphisms (SNPs) from pooled sequencing. 2. It identifies both rare and common variants.
Bansal V. A statistical method for the detection of variants from next-generation resequencing of DNA pools. Bioinformatics. 2010 Jun 15;26(12):i318-24. PubMed PMID: 20529923; PubMed Central PMCID: PMC2881398.
2010
100
Crossbow
http://bowtie-bio.sourceforge.net/crossbow/
1. Used for SNP detection. 2. Combines Bowtie and SoapSNP Analyzes data comprising 38-fold coverage of the human genome in three hours using a 320-CPU.
Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL. Searching for SNPs with cloud computing. Genome Biol. 2009;10(11):R134. Epub 2009 Nov 20. PubMed PMID: 19930550.
2009
100
dbSNP
http://www.ncbi.nlm.nih.gov/snp/
1. It includes single nucleotide substitutions, small insertion/deletion polymorphisms, invariant regions of sequence, microsatellite repeats, named variants <0.001% and uncharacterized heterozygous assays. 2. It contains original submission records and reference SNP records. 3. Reference SNP records has variation summary. 4. It contains data from Watson, venter and Korean individual.
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PubMed PMID: 11125122; PubMed Central PMCID: PMC29783.
2001
100
DIAL - De novo Identification of Alleles
http://www.bx.psu.edu/miller_lab/
1. DIAL (De novo Identification of Alleles), for identifying single-base substitutions between two closely related genomes without the help of a reference genome. 2. The method works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to determine small insertions/deletions. 3. The use of DIAL to identify nucleotide differences among transcriptome sequences.
Ratan A, Zhang Y, Hayes VM, Schuster SC, Miller W. Calling SNPs without a reference sequence. BMC Bioinformatics. 2010 Mar 15;11:130. PMID: 20230626
2010
100
Requires installation of LASTZ in the path.
DiBayes
http://solidsoftwaretools.com/gf/project/dibayes/
1. Used for SNP discovery 2. Uses bayesian identification of SNPs for color space (SOLiD) data.
Not available
Not available
100
URL is not working and a message "This webpage will be removed on May 15, 2012" is seen, as on 9th May 2012.
DNA Baser
http://www.dnabaser.com/
1. Used for detecting structural variation. 2. Portable and does not require installation. 3. Can be used for both manual and automatic sequence assembly, analysis, editing, sample processing, metadata integration, file format conversion and mutation detection.
Not available
Not available
100
Request has to be sent for the free download of the software.
DNAA
http://sourceforge.net/apps/mediawiki/dnaa/index.php?title=Main_Page
Used for structural variant analysis, SNP discovery and DNA Methylation analysis.
Not available
Not available
100
Requires installation of SAMtools in the path.
FindPeaks
http://sourceforge.net/apps/mediawiki/vancouvershortr/index.php?title=FindPeaks
1. Used for genomics, SNP discovery. 2. Contains the 'FindPeaks' application for Chip-Seq and RNA-Seq analysis. 3. It has a nascent database for storing SNPs across multiple libraries.
Fejes, AP, Robertson, G, Bilenky, M, Varhol, R, Bainbridge, M, Jones, SJ (2008). FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics, 24, 15:1729-30.[PMID: 18599518]
2008
100
FreeBayes
http://bioinformatics.bc.edu/marthlab/FreeBayes
It is an efficient, flexible software for variant detection plus SNP and indel calling.
Not available
Not available
100
Galaxy
http://main.g2.bx.psu.edu/
1. It is an open web based software to perform computational analysis of genomic data. 2. It allows user to repeat, store and annotate the analysized data in an interactive web based format. 3. It has tools for QC and manipulation, mapping tools like Bowtie (Illumina, SOLiD), LASTZ, Megablast (Roche 454), BWA (Illumina, SOLiD), SAMTools, TopHat, Cufflinks for RNA analysis. 4. It doesn't need any programming knowledge.
Taylor J, Schenck I, Blankenberg D, Nekrutenko A. Using galaxy to perform large-scale interactive data analyses. Curr Protoc Bioinformatics. 2007 Sep;Chapter 10:Unit 10.5. PubMed PMID: 18428782.
2007
100
galign
http://shahamlab.rockefeller.edu/galign
1. Used for SNP discovery. 2. Has alignment method, SNP search, deletion search, simple SNP, Format convert, genome assemble, identifies polymorphisms between sequence reads obtained using Illumina/Solexa technology and a reference genome.
Shaham S. galign: a tool for rapid genome polymorphism discovery. PLoS One. 2009 Sep 25; 4(9):e7188. PubMed PMID: 19779626; PubMed Central PMCID: PMC2746318
2009
100
GAMES
http://aqua.unife.it/GAMES/
1. Used for SNP discovery, SNP Annotation, InDel detection, identification of mis-matches with clinical significance. 2. Predicts functional effects of mutation.
Sana ME, Iascone M, Marchetti D, Palatini J, Galasso M, Volinia S. GAMES identifies and annotates mutations in next-generation sequencing projects. Bioinformatics. 2011 Jan 1;27(1):9-13. Epub 2010 Oct 22. PubMed PMID: 20971986
2011
100
GATK - Genome Analysis Toolkit
http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit
1. The Genome Analysis Toolkit (GATK) is a software package which can perform various NGS analysis. 2. It solves the data management challenge by separating data access patterns from analysis algorithms, using the functional programming philosophy of Map/Reduce.
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010 Sep;20(9):1297-303. Epub 2010 Jul 19. PubMed PMID: 20644199; PubMed Central PMCID: PMC2928508.
2010
100
Geneious
http://www.geneious.com/
1. The Geneious Pro sequence viewer is a landmark innovation in the field of sequence analysis and is a critical feature that differentiates Geneious Pro from all other competitors. 2. Geneious chooses the viewers which suit the selected data automatically. 3. It displays DNA and protein sequences with annotations alongside sequences and visualize your entire contig of regular or NGS sequence data and zoom right down the nucleotide level to identify SNPs, regions of low/high coverage, or other interesting biological features. 4. It displays sequences with their sequence traces and visualize the success of your experiment with the quality score coloring scheme.
Not available
Not available
100
Free trial downloadable version is available for 14 days.
GigaBayes
http://bioinformatics.bc.edu/marthlab/GigaBayes
1. Used for SNP discovery and short indel discovery. 2. Extremely fast and flexible mapping algorithm, allowing for multiple insertions or deletions. 3. Helps in mapping to genomes and transcriptomes of 25 organisms.
Not available
Not available
100
Replaced by FreeBayes.
GMS - Genomatix Mining Station
http://www.genomatix.de/en/index.html
1. It has highest quality results within shortest time. 2. Used in RNA-Seq, non-coding RNA-Seq, assembly, SNP discovery and ChIP-Seq analysis. 3. Allows multiple insertions or deletions, maps genomes and transcriptomes of 25 organisms. 4. It supports sequence and color-based tags from Illumina (Genome Analyzer and HiSeq), SOLiD, Helicos and 454 Life Sciences Sequencers.
Not available
Not available
100
HeliSphere
http://open.helicosbio.com/
1. Used in genomics, whole genome resequencing, RNA-Seq, SNP discovery. 2. Helps in alignment of reads to a reference, filtering of reads or alignments, report generation, file format conversions, etc. 3. Produced by the HeliScope Single Molecule Sequencer.
Not available
Not available
100
Illuminator
http://dna.leeds.ac.uk/illuminator/
It is used to find variations in illumina short reads.
Carr IM, Morgan JE, Diggle CP, Sheridan E, Markham AF, Logan CV, Inglehearn CF, Taylor GR, Bonthron DT. Illuminator, a desktop program for mutation detection using short-read clonal sequencing. Genomics. 2011 May 19. [Epub ahead of print] PubMed PMID: 21621601.
2011
100
It is still under development.
inGAP
http://sourceforge.net/projects/ingap/
1. InGAP, which is guided by a Bayesian principle to detect single nucleotide polymorphisms, insertion and deletions by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. 2. It can also help with completing genome assembly and comparative genome analysis. 3. InGAP can detect SNPs and indels by comparing sequence data generated by either Roche/454 and/or Illumina sequencing technologies, with a reference sequence, regardless read lengths and numbers.
Qi J, Zhao F, Buboltz A, Schuster SC. inGAP: an integrated next-generation genome analysis pipeline. Bioinformatics. 2010 Jan 1;26(1):127-9. Epub 2009 Oct 30. PubMed PMID: 19880367; PubMed Central PMCID: PMC2796817.
2010
100
kisSnp
http://alcovna.genouest.org/kissnp-page/
1. A tool which compares 2 sets of short reads from next generation technology and finding SNP between them. 2. The 2 sets of reads are from 2 individuals of same or related species.
P.Peterlongo, N.Schnel, N.Pisanti, M.-F. Sagot, V.Lacroix: Identifying SNPs without a reference genome by comparing raw reads. Proceedings of String Processing and Information Retrieval (SPIRE) 2010, Springer LNCS.
2010
100
Lasergene
http://www.dnastar.com/t-sub-products-lasergene-editseq.aspx
It is used for alignment, de novo sequencing, de-novo assembly, genomics, integrated solution, mapping, phylogenetics, protein structure analysis, read alignment, SNP discovery, SNP/Indel detection, sequence analysis and transcription factor binding site identification.
Not available
Not available
100
Request has to be sent for the free download of the software for Windows and Mac OS X.
MapNext
http://evolution.sysu.edu.cn/english/software/mapnext.htm
1. Facilitate the conversion of text based output into a SQL database. 2. Provides useful information about the SNP detection from population sequences. 3. Used for RNA-Seq Alignment.
Bao H, Xiong Y, Guo H, Zhou R, Lu X, Yang Z, Zhong Y, Shi S. MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads. BMC Genomics. 2009 Dec 3;10 Suppl 3:S13. PubMed PMID: 19958476; PubMed Central PMCID: PMC2788365.
2009
100
MAQ - Mapping and Assembly with Quality
http://maq.sourceforge.net
1. MAQ is used for aligning reads to reference sequences and then calls the consensus. It performs ungapped alignment. 2. It also performs assembly by calling the consensus based on a statistical model. 3. MAQ is used for SNP calling in the nucleotide space by converting color alignment to nucleotide alignment. 4. It does not consider the mapping quality of reads containing mutations, which will lead to high false negative rates due to the strategy used in calling SNPs. 5. It has two commands which will extract information from binary files: a) cns2ref extracts the reference sequences from the consensus file. b) cns2fq extracts the consensus sequences and their qualities.
Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008 Nov;18(11):1851-8. Epub 2008 Aug 19. PMID: 18714091
2008
100
MAQGene
http://maqweb.sourceforge.net/
1. Used for SNP discovery. 2. Complete pipeline for mutant discovery, with web front end. 3. Classifies each found mutation based on its canonically predicted effect on the coding sequence. 4. Identifies reads from illumina platform.
Not available
Not available
100
Margarita
http://www.sanger.ac.uk/resources/software/margarita/
Used for SNP discovery, genotyping from low coverage sequencing data.
Minichiello MJ, Durbin R. Mapping trait loci by use of inferred ancestral recombination graphs. Am J Hum Genet. 2006 Nov;79(5):910-22. Epub 2006 Sep 27. PubMed PMID: 17033967; PubMed Central PMCID: PMC1698562.
2006
100
MIRA
http://sourceforge.net/apps/mediawiki/mira-assembler/index.php
1. MIRA 3 is able to perform true hybrid de novo assemblies using reads gathered through Sanger, 454 or Solexa sequencing technologies. 2. It assembles reads instead of a mix of shredded consensus sequence and reads. 3. MIRA 3 is for assembly of genomic data as well as assembly of EST data from one or multiple strains/organisms and MIRA searches EST SNPs for assembly of EST data from different strains (or organisms) and SNP detection within this assembly.
Chevreux et al. (1999) Genome Sequence Assembly Using Trace Signals and Additional Sequence Information Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
1999
100
MoDIL - Mixture of Distributions Indel Locator
http://compbio.cs.toronto.edu/modil/
1. MoDIL says to be the first method to identify medium size (20-50 bp) indels from high-throughput sequencing data while there exists several methods identifying small and large indels. 2. As an input MoDIL takes sequence reads. MoDIL uses EM algorithm  and Kolmogorov-Smirnov test while doing the analysis. As an output program it gives identified indels.
Lee S, Hormozdiari F, Alkan C, Brudno M. MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions. Nat Methods. 2009 Jul;6(7):473-4. Epub 2009 May 31. PMID: 19483690
2009
100
Nesoni
http://www.bioinformatics.net.au/software.nesoni.shtml
1. Used to determine the protein level changes resulting from SNPs and indels, to find differences between multiple strains, or to produce n-way comparison data suitable for phylogenetic analysis in SplitsTree4. 2. Used largely for bacterial genomes.
Not available
Not available
100
NextGENe
http://www.softgenetics.com/NextGENe.html
NextGENe contains analysis modules for SNP/INDEL & Structural Variant Analysis, Deep Sequencing, Whole Genome Alignment, RNA Seq, ChipSeq, miRNA Analysis, Metagenomic and de novo assembly.
Not available
Not available
100
ngs_backbone
http://bioinf.comav.upv.es/ngs_backbone/index.html
1. It is capable of cleaning reads, de novo assembly or mapping against a reference and annotate SNPs, SSRs, ORFs. 2. Used in transcriptome analysis and sometimes in genome analysis.
Not available
Not available
100
Omixon Variant Toolkit
https://www.omixon.com/omixon/index.htm
1. Easy to use and highly accurate set of tools for detecting micro indels and SNP. 2. Aligns, maps and calls variants for color reads against a reference genome. 3. Runs on the Amazon Cloud.
Not available
Not available
100
PanGEA
http://www.kofler.or.at/bioinformatics/PanGEA/
1. PanGEA can be used for the analysis of gene expression using next-generation sequencing technologies. 2. Transcriptome profiling using next-generation sequencing technologies has several advantages compared to the well established method: microarrays platform. 3. Using sequences, allele specific gene-expression, alternative splicing, inter-species differences in gene expression, and relative expression levels between genes can easily be investigated.
Kofler R, Teixeira Torres T, Lelley T, Schlotterer C. PanGEA: identification of allele specific gene expression using the 454 technology. BMC Bioinformatics. 2009 May 14;10:143. PMID: 19442283
2009
100
PolyBayesShort
http://bioinformatics.bc.edu/marthlab/PbShort
Optimized for the analysis of large numbers (millions) of high-throughput next-generation sequencer reads, aligned to whole chromosomes of model organism or mammalian genomes.
Marth GT, Korf I, Yandell MD, Yeh RT, Gu Z, Zakeri H, Stitziel NO, Hillier L, Kwok PY, Gish WR. A general approach to single-nucleotide polymorphism discovery. Nat Genet. 1999 Dec;23(4):452-6. PubMed PMID: 10581034.
1999
100
PolyScan
http://genome.wustl.edu/software/polyscan
1. A software tool specially designed to provide de novo indel detection and SNP identification in the context of high-throughput medical sequencing. 2. PolyScan starts the analysis from the raw chromatograms and re-basecall signals in the each of the fluorescence channels. 3. This feature makes PolyScan applicable to both polymorphism and mutation discovery, which requires analyzing of small intensity signals. 4. Alignment and Bayesian probabilistic methods are used to compute probabilities of SNPs as well as small and medium-sized indels (< 100bp).
Chen K, McLellan MD, Ding L, Wendl MC, Kasai Y, Wilson RK, Mardis ER. PolyScan: an automatic indel and SNP detection approach to the analysis of human resequencing data. Genome Res. 2007 May;17(5):659-66. Epub 2007 Apr 6. PubMed PMID: 17416743; PubMed Central PMCID: PMC1855178.
2007
100
ProbHD
http://www.mcb.mcgill.ca/~blanchem/reseq/
1. Used for identifying heterozygous sites in a single individual by using a machine learning approach that generates a heterozygosity score for each chromosomal position. 2. Helps in the identification of regions with unequal representation of two alleles and other poorly sequenced regions.
Hoberman R, Dias J, Ge B, Harmsen E, Mayhew M, Verlaan DJ, Kwan T, Dewar K, Blanchette M, Pastinen T. A probabilistic approach for SNP discovery in high-throughput human resequencing data. Genome Res. 2009 Sep;19(9):1542-52. Epub 2009 Jul 15. PubMed PMID: 19605794; PubMed Central PMCID: PMC2752119.
2009
100
PyroBayes
http://bioinformatics.bc.edu/marthlab/PyroBayes
1. PyroBayes is a novel base caller for pyrosequences from the 454 sequencing machines. 2. Pyrobayes permits accurate SNP calling in re-sequencing applications, even in shallow read coverage, primarily because it produces more confident base calls than the native base calling program. 3. It produces more accurate higher base qualities and hence make more high quality base calls in 454 pyrosequences. 4. It produces base qualities up to 50. Pyrobayes can process a single sequencing run in under 2 minutes.
Quinlan AR, Stewart DA, Strömberg MP, Marth GT. Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nat Methods. 2008 Feb;5(2):179-81. Epub 2008 Jan 13. PubMed PMID: 18193056.
2008
100
QCALL
ftp://ftp.sanger.ac.uk/pub/rd/QCALL
SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples.
Not available
Not available
100
R2R - Reads to Results
http://milne.ruc.dk/R2R/
1. Simple to use package for very sensitive analysis of short read sequence data obtained by NextGen sequencing techniques. 2. Developed in conjunction with data obtained on the Illumina GA platforms. 3. Written in simple Perl script and runs equally well under MS Windows, Mac OS and Linux/Unix operative systems.
Not available
Not available
100
SAMtools
http://samtools.sourceforge.net
Various utilities for processing alignments in the SAM format, including variant calling and alignment viewing.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. Epub 2009 Jun 8.PMID: 195059
2009
100
SeqEM
http://hihg.med.miami.edu/software-download/seqem-version-1.0
1. SeqEM is a SNP calling algorithm for next generation sequencing data. 2. It uses EM algorithm for parameter estimation for next generation sequencing data of unrelated individual samples. 3. It can estimate error rate of the reads and frequency of genotypes. 4. It also helps in disease association studies by classification of genotypes.
Martin ER, Kinnamon DD, Schmidt MA, Powell EH, Zuchner S, Morris RW. SeqEM: an adaptive genotype-calling approach for next-generation sequencing studies. Bioinformatics. 2010 Nov 15;26(22):2803-10. Epub 2010 Sep 21. PubMed PMID: 20861027; PubMed Central PMCID: PMC2971572.
2010
100
SeqGene
http://sourceforge.net/apps/mediawiki/seqgene/index.php?title=SeqGene
1. It is an open source software mainly used for quality control, SNP annotation and indel identification, RNA Seq expression analysis, allele specific expression, genotype analysis and pathway analysis. 2. It takes aligned SAM reads as input. 3. It can perform differential expression from the RNA seq data.
Deng X. SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data. BMC Bioinformatics. 2011 Jun 29;12:267. PubMed PMID: 21714929; PubMed Central PMCID: PMC3148209.
2011
100
Requires installation of R 2.10 or above (optional for differential expression analysis), Bioconductor packages such as hash, graph, RBGL, KEGGgraph, Rgraphviz, org.Hs.eg.db, org.Rn.eg.db, org.Mm.eg.db (optional for pathway analysis in RNA-Seq) in the path.
SeqMan NGen
http://www.dnastar.com/t-products-seqman-ngen.aspx
1. It is used for SNP discovery, Sequence assembly, coverage evaluation and consensus annotation. 2. It has integration with Lasergene.
Not available
Not available
100
Slider
http://www.bcgsc.ca/platform/bioinfo/software/slider
1. Slider is an alignment tool used for reducing alignment problems by making use of probability of reads in prb files. 2. It has high efficiency and accuracy for alignment and SNP prediction. 3. It can reduce the mis-match percentage in bases.
Malhis N, Butterfield YS, Ester M, Jones SJ.Slider--maximum use of probability information for alignment of short sequence reads and SNP detection.Bioinformatics. 2009 Jan 1;25(1):6-13. Epub 2008 Oct 30. PMID: 18974170.
2009
100
SliderII
http://www.bcgsc.ca/platform/bioinfo/software/SliderII
1. High quality SNP calling using Illumina data at minimal coverage. 2. Calibrate prb data before calling SNPs. 3. Utilize information about known SNPs of a target genome.
Malhis N, Jones SJ. High quality SNP calling using Illumina data at shallow coverage. Bioinformatics. 2010 Apr 15;26(8):1029-35. Epub 2010 Feb 26. PubMed PMID: 20190250.
2010
100
SNIP-Seq
http://www.stsiweb.org/index.php/infrastructure/software_data/variant_detection_from_population_scale_sequence_data_snip_seq/
1. It is a tool for discovering SNPs in population sequencing data. 2. It assigns genotype to individuals. 3. It has low false SNP detection rate less than 2%.
Bansal V, Harismendy O, Tewhey R, Murray SS, Schork NJ, Topol EJ, Frazer KA. Accurate detection and genotyping of SNPs utilizing population sequencing data. Genome Res. 2010 Apr;20(4):537-45. Epub 2010 Feb 11. PubMed PMID: 20150320; PubMed Central PMCID: PMC2847757.
2010
100
Sniper - SNP identification using Probability of Every Read
http://kim.bio.upenn.edu/software/sniper.shtml
It is a SNP discovery tool which uses bayesian probabilistic model that identifies SNPs in both repetitive and unique regions of a genome from multi mapped sequence reads.
Simola DF, Kim J. Sniper: improved SNP discovery by multiply mapping deep sequenced reads. Genome Biol. 2011 Jun 20;12(6):R55. [Epub ahead of print] PubMed PMID: 21689413.
2011
100
SNP-o-matic
http://snpomatic.sourceforge.net/
1. It is used for the analysis of Solexa reads and compares to the references sequence to find the known SNPs. 2. It is a stringent read mapping tool using indexing algorithm.
Manske HM, Kwiatkowski DP. SNP-o-matic. Bioinformatics. 2009 Sep 15;25(18):2434-5. Epub 2009 Jul 2. PubMed PMID: 19574284; PubMed Central PMCID: PMC2735664.
2009
100
SNPSeeker
http://www.genetics.wustl.edu/rmlab/software.htm
1. Identification of SNPs in pooled genomic samples. 2. It identify data generated from illumina platform.
Druley TE, Vallania FL, Wegner DJ, Varley KE, Knowles OL, Bonds JA, Robison SW, Doniger SW, Hamvas A, Cole FS, Fay JC, Mitra RD. Quantification of rare allelic variants from pooled genomic DNA. Nat Methods. 2009 Apr;6(4):263-5. Epub 2009 Mar 1. PubMed PMID: 19252504; PubMed Central PMCID: PMC2776647.
2009
100
Replaced by SPLINTER.
SNVMix
http://compbio.bccrc.ca/software/snvmix/
1. Detects single nucleotide variants from next generation sequencing data. 2. Post alignment tool. 3. SNVMix will output the probability that each position is one of three genotypes (homozygous for the reference allele, heterozygous, homozygous for a non-reference allele).
Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP. SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Bioinformatics. 2010 Mar 15;26(6):730-6. Epub 2010 Feb 3. PubMed PMID: 20130035; PubMed Central PMCID: PMC2832826.
2010
100
SOAPsnp
http://soap.genomics.org.cn/soapsnp.html
Mainly used for re-sequencing that can assemble consensus sequence for the genome on the known reference. Can identify SNPs.
Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J. SNP detection for massively parallel whole-genome resequencing. Genome Res. 2009 Jun;19(6): 1124-32. Epub 2009 May 6. PubMed PMID: 19420381; PubMed Central PMCID: PMC2694485.
2009
100
SOCS
http://solidsoftwaretools.com/gf/project/socs/
1. SOCS is a reference-based, ungapped alignment tool designed for mapping both standard SOLiD data and bisulfite transformed SOLiD data. 2. Short sequence-space variants of a user-specified length (typically one for SNPs) can be inferred from valid color-space variants.
Ondov BD, Varadarajan A, Passalacqua KD, Bergman NH. Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications. Bioinformatics. 2008 Dec 1;24(23):2776-7. Epub 2008 Oct 7. PMID: 18842598
2008
100
Solid-genotyper
http://www.hgsc.bcm.tmc.edu/cascade-tech-software_solid_genotyper-ti.hgsc
1. Solid-genotyper is a SNP discovery and genotyping tool for high coverage SOLiD data. 2. This tool combines a logistics regression model and heuristic methods to characterize systematic sequencing error and overcome mapping bias issue.
Not available
Not available
100
SomaticSniper
http://genome.wustl.edu/software/somaticsniper
1. This program is to identify single nucleotide positions that are different between tumor and normal (or, in theory, any two BAM files). 2. It takes a tumor BAM and a normal BAM and compares the two, to determine the differences. 3. It uses the genotype likelihood model of MAQ (as implemented in SAMTools) and then calculates the probability that the tumor and normal genotypes are different.
Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, Ley TJ, Mardis ER, Wilson RK, Ding L. SomaticSniper: Identification of Somatic Point Mutations in Whole Genome Sequencing Data. Bioinformatics. 2011 Dec 6. [Epub ahead of print] PubMed PMID: 22155872.
2011
100
SRMA - short read micro re-aligner
http://srma.sourceforge.net
1. SRMA is a short read micro re-aligner for next-generation high throughput sequencing data. 2. This tool aims to perform a re-alignment of each read to a graphical representation of all alignments within a local region to provide a better overall base-resolution consensus. 3. SRMA does not support enumerating over insertions or deletions caused by homopolymer errors that can be found in 454 data and other flow-based technologies.
Homer N, Nelson SF. Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA. Genome Biol. 2010;11(10):R99. Epub 2010 Oct 8. PMID: 20932289
2010
100
ssahaSNP
http://www.sanger.ac.uk/resources/software/ssahasnp/
Polymorphism detection tool. Detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence.
Not available
Not available
100
SWAP454
http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/computational-research-and-development
1. SWAP454 is a program for calling SNPs using 454 read data. It aligns to the genome using a novel alignment tool called QueryLookupTable, and looks for unique alignments to a reference. 2. Using those alignments, a coverage map file is built that indicates the coverage and base calls for each base position on the reference. This coverage is filtered using a neighborhood-quality score method. 3. The coverage map file can be transformed into individual SNP calls. SWAP454 also includes code for creating improved quality scores for 454 read data that has been incorporated into the algorithm used by 454 Life Sciences.
Brockman W, Alvarez P, Young S, Garber M, Giannoukos G, Lee WL, Russ C, Lander ES, Nusbaum C, Jaffe DB. Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res. 2008 May;18(5):763-70. Epub 2008 Jan 22. PMID: 18212088
2008
100
Syzygy
http://www.broadinstitute.org/software/syzygy/
1. Aligns to the genome using a novel alignment tool called QueryLookupTable, and looks for unique alignments to a reference. 2. Includes code for creating improved quality scores for 454 read data.
Not available
Not available
100
VAAL - Variant Ascertainment Algorithm
http://www.mybiosoftware.com/sequence-analysis/1246
1. A variant ascertainment algorithm that can be used to detect SNPs, indels, and more complex genetic variants. High sensitivity on bacterial data sets. 2. Compare reads from one strain to a reference sequence from another strain. 3. Compare reads from two strains to each other, using a third strain to determine homology.
Nusbaum C, Ohsumi TK, Gomez J, Aquadro J, Victor TC, Warren RM, Hung DT, Birren BW, Lander ES, Jaffe DB. Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. Nat Methods. 2009 Jan;6(1):67-9. Epub 2008 Dec 14. PubMed PMID: 19079253; PubMed Central PMCID: PMC2613166.
2009
100
VARiD - Variation Detection
http://compbio.cs.utoronto.ca/varid/
1.Detect SNP and indel from SOLiD color space and regular letter space reads. 2. Identify heterozygous, homozygous and tri-allelic SNPs, as well as micro-indels.
Dalca AV, Rumble SM, Levy S, Brudno M. VARiD: a variation detection framework for color-space and letter-space platforms. Bioinformatics. 2010 Jun 15;26(12):i343-9. PubMed PMID: 20529926; PubMed Central PMCID: PMC2881369.
2010
100
Varietas
http://kokki.uku.fi/bioinformatics/varietas/
1. It has details on SNP, CNV and indels in batches. 2. It also gives details about related genes, phenotypes and disease. 3. It receives data from Ensembl genome database, NCBI dbSNP database, The Genomic Association Database (GAD), OMIM, WikiGenes and SNPedia. 4. It converts SNPs to gene sets.
Paananen J, Ciszek R, Wong G. Varietas: a functional variation database portal. Database (Oxford). 2010 Jul 29;2010:baq016. Print 2010. PubMed PMID: 20671203; PubMed Central PMCID: PMC2997604.
2010
100
VarScan
http://varscan.sourceforge.net/
1. VarScan is able to detect SNPs and indels from both Solexa and Roche platforms. 2. Unlike currently available variant detection tools, VarScan is compatible with several read aligners (BLAT, Newbler, cross_match, Bowtie and Novoalign) and calls variants in both individual and pooled samples. 3. As an input VarScan requires an alignment file. As an output, user gets reports of SNPs, insertions and deletions with their chromosomal coordinates, alleles, flanking sequence and read counts.
Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics. 2009 Sep 1;25(17):2283-5. Epub 2009 Jun 19. PMID: 19542151
2009
100
VIP - Variant Identification Pipeline
http://athos.ugent.be/VIP_pipeline
1. Used for mapping, SNP calling, coverage analysis and SNP annotation. 2. Used for analysis of 454/Roche GS-FLX amplicon re-sequencing experiments that enables variation detection, variation detection validation, PCR efficiency optimization and allows optimization of the multiplex PCR, used to amplify the amplicons.
De Schrijver JM, De Leeneer K, Lefever S, Sabbe N, Pattyn F, Van Nieuwerburgh F, Coucke P, Deforce D, Vandesompele J, Bekaert S, Hellemans J, Van Criekinge W. Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline. BMC Bioinformatics. 2010 May 20;11:269. PubMed PMID: 20487544; PubMed Central PMCID: PMC2880033.
2010
100
 
Disclaimer
Grow and let grow!
copyright © shodhaka life sciences private limited; all rights reserved

Internet Coupons
xanga traffic