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A compilation and categorization of next-generation sequencing resources : RNA seq alignment
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
Oases
http://www.ebi.ac.uk/~zerbino/oases/
1. Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. 2. Oases uploads a preliminary assembly produced by Velvet, and clusters the contigs into small groups, called loci. 3. It then exploits the paired-end read and long read information, when available, to construct transcript isoforms.
Schulz M, Zerbino D: Oases - De novo transcriptome assembler for very short reads.Tech. rep., MPI for Molecular Genomics, European Bioinformatics Institute (EMBL-EBI), UC Santa Cruz 2010.
2010
96
PALMA
http://www.fml.tuebingen.mpg.de/raetsch/suppl/palma
1. A novel approach based on large margin learning that combines accurate splice site predictions with common sequence alignment techniques. 2. By solving a convex optimization problem, algorithm called PALMA tunes the parameters of the model such that true alignments score higher than other alignments. 3. It identifies the intron boundaries as well as boundaries of the optimal local alignment. 4. This method also demonstrates robustness to mutations, insertions and deletions, retaining accuracy even at high noise levels.
Schulze U, Hepp B, Ong CS, Ratsch G. PALMA: mRNA to genome alignments using large margin algorithms. Bioinformatics. 2007 Aug 1;23(15):1892-900. Epub 2007 May 30. PMID: 17537755
2007
97
ABMapper
http://abmapper.sourceforge.net/
1. Maps RNA-Seq reads to target genome, considering possible multiple mapping locations and splice junctions. 2. Detects exonic alignment. 3. It has overlap parameter.
Lou SK, Ni B, Lo LY, Tsui SK, Chan TF, Leung KS. ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping. Bioinformatics. 2011 Feb 1;27(3):421-2. Epub 2010 Dec 17. PubMed PMID: 21169377; PubMed Central PMCID: PMC3031031.
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
CPTRA
http://people.tamu.edu/~syuan/cptra/cptra.html
1. CPTRA is Cross Platform TRanscriptome Analysis. 2. It is used for analyzing transcriptome data. 3. It can be used for analysis of species where reference genome is unavailable. 4. It is also used for RNA seq quantitation.
Zhou X, Su Z, Sammons RD, Peng Y, Tranel PJ, Stewart CN Jr, Yuan JS. Novel software package for cross-platform transcriptome analysis (CPTRA). BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S16. PubMed PMID: 19811681.
2009
100
Cufflinks
http://cufflinks.cbcb.umd.edu/
1. It assembles transcripts and estimates their abundances in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. 2. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one. 3. Cufflinks implements a constructive proof of Dilworth's Theorem by constructing a covering relation on the read alignments, and finding a minimum path cover on the directed acyclic graph for the relation. Works well with unpaired RNA-Seq reads.
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010 May;28(5):511-5. Epub 2010 May 2. PubMed PMID: 20436464.
2010
100
Requires installation of Boost C++ libraries and SAMtools.
ERANGE
http://woldlab.caltech.edu/rnaseq/
1. It can perform both RNA seq analysis and ChIP seq analysis. 2. It can also perform allele specific transcription.
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008 Jul;5(7):621-8. Epub 2008 May 30. PubMed PMID: 18516045.
2008
100
est2assembly
http://code.google.com/p/est2assembly/
1. Tool used for de novo assembly and annotation. 2. It has a Gbrowse feature.
Papanicolaou A, Stierli R, Ffrench-Constant RH, Heckel DG. Next generation transcriptomes for next generation genomes using est2assembly. BMC Bioinformatics. 2009 Dec 24;10:447. PubMed PMID: 20034392; PubMed Central PMCID: PMC3087352.
2009
100
FreClu - FREquencing based de Novo short read CLUstering
http://mlab.cb.k.u-tokyo.ac.jp/~quwei/DeNovoShortReadClustering/
1. Novel, massively parallel sequencing technologies provide a highly detailed structure of transcriptome and genome by yielding deep coverage of short reads, though their utility is interfered due to a considerable sequencing quality problem and short length of reads. 2. Sequencing-error trimming in short reads is therefore a vital process which could improve the successful rate of reference mapping as well as polymorphorism detection. 3. This algorithm organizes erroneous short sequences, originating in a single abundant sequence into a tree structure such that each child sequence is considered to be derived stochastically from its more abundant parent sequence because of sequencing errors.
Qu W, Hashimoto S, Morishita S. Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing. Genome Res. 2009 Jul;19(7):1309-15. Epub 2009 May 13. PubMed PMID: 19439514; PubMed Central PMCID: PMC2704438.
2009
100
G-Mo.R-Se -Gene MOdeling using RNA-Seq
http://www.genoscope.cns.fr/externe/gmorse/
1. It is used to build de novo genes from RNA seq data. 2. It is Gene Modelling using RNA Seq.
Denoeud F, Aury JM, Da Silva C, Noel B, Rogier O, Delledonne M, Morgante M, Valle G, Wincker P, Scarpelli C, Jaillon O, Artiguenave F. Annotating genomes with massive-scale RNA sequencing. Genome Biol. 2008;9(12):R175. Epub 2008 Dec 16. PubMed PMID: 19087247; PubMed Central PMCID: PMC2646279.
2008
100
Still in development, but currently unstable version is available.
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
GSNAP - Genomic Short-read Nucleotide Alignment Program
http://research-pub.gene.com/gmap/
1. GSNAP is Genomic Short-read Nucleotide Alignment Program. 2. It can align paired-end and single-end data. 3. It can be used to detect splicing.
Wu TD, Nacu S. Fast and SNP tolerant detection of complex variants and splicing in short reads. Bioinformatics. 2010 Apr 1;26(7):873-81. Epub 2010 Feb 10. PubMed PMID: 20147302; PubMed Central PMCID: PMC2844994.
2010
100
HMMSplicer
http://derisilab.ucsf.edu/index.php?software=105
1. A tool used to discover splice junction in short reads from next generation sequencing platforms. 2. More accurate than existing tools. 3. It can discover splice junction on genes with low expression.
Dimon MT, Sorber K, DeRisi JL. HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data. PLoS One. 2010 Nov 8;5(11):e13875. PubMed PMID: 21079731; PubMed Central PMCID: PMC2975632.
2010
100
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
MapPER
http://www.netlab.uky.edu/p/bioinfo/MapPER
1. It is an integrated version of mapsplice pipeline. 2. It can work well with paired-end datasets.
Hu Y, Wang K, He X, Chiang DY, Prins JF, Liu J. A probabilistic framework for aligning paired-end RNA-seq data. Bioinformatics. 2010 Aug 15;26(16):1950-7. Epub 2010 Jun 23. PubMed PMID: 20576625; PubMed Central PMCID: PMC2916723.
2010
100
MapSplice
http://www.netlab.uky.edu/p/bioinfo/MapSplice
1. It is mainly used to discover splice junction. 2. It can align short and long reads. 3. It can detect exons and chimeric events in long and short reads. 4. It can make use of paired-end data.
Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res. 2010 Oct;38(18):e178. Epub 2010 Aug 27. PubMed PMID:20802226; PubMed Central PMCID:PMC2952873.
2010
100
MicroRazerS
www.seqan.de/projects/microrazers.html
1. It is a small RNA mapping tool which is faster than the mega BLAST. 2. It can map easily short RNAs to the reference genome and find SNPs and sequencing errors. 3. It is useful for identification and quantification of miRNAs.
Emde AK, Grunert M, Weese D, Reinert K, Sperling SR. MicroRazerS: rapid alignment of small RNA reads. Bioinformatics. 2010 Jan 1;26(1):123-4. Epub 2009 Oct 29. PubMed PMID: 19880369.
2010
100
miRanalyzer
http://web.bioinformatics.cicbiogune.es/microRNA/miRanalyser.php
1. It is a free online tool for the mapping of small RNAs against known micro RNAs and non coding RNAs. 2. It can identify genes with new micro RNAs and are differentially expressed. 3. It can find perfect matches of all transcribed sequences and detects the known annotated microRNAs in miRBase.
Hackenberg M, Sturm M, Langenberger D, Falcon-Perez JM, Aransay AM. miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W68-76. Epub 2009 May 11. PubMed PMID: 19433510; PubMed Central PMCID: PMC2703919.
2009
100
Myrna
http://bowtie-bio.sourceforge.net/myrna/index.shtml
1. It is a tool used for differential gene expression analysis. 2. It needs Bowtie for alignment. 3. It also needs R/bioconductor package for statistical calculations.
Langmead B, Hansen KD, Leek JT. Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol. 10;11(8):R83. Epub 2010 Aug 11. PubMed PMID: 20701754; PubMed Central PMCID: PMC2945785.
2010
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
Novoalign
http://www.novocraft.com/main/index.php
1. Alignment tool for aligning short sequences against an indexed set of reference sequences. 2. Aligning Illumina single-end and paired-end reads. 3. Gapped alignment on single-end reads and paired-end reads 4. Single pass alignment for Bisulphite treated DNA.
Not available
Not available
100
PALMapper
http://www.fml.tuebingen.mpg.de/raetsch/suppl/palmapper
1. It has properties of GenomeMapper and PALMapper. 2. It can handle mismatches and indels.
Jean G, Kahles A, Sreedharan VT, De Bona F, Rätsch G. RNA-Seq read alignments with PALMapper. Curr Protoc Bioinformatics. 2010 Dec;Chapter 11:Unit 11.6. PubMed PMID: 21154708.
2010
100
QPALMA
http://www.fml.mpg.de/raetsch/projects/qpalma
1. Alignment tool targeted to align spliced reads produced by Next Generation Sequencing platforms such as Illumina Solexa or 454. 2. Aligns short reads to the genomic sequences in an optimal way according to its underlying algorithm and trained parameters. 3. Creates an alignment using dynamic programming (written in C++), and returns the alignment in a PSL like format.
De Bona F, Ossowski S, Schneeberger K, Rätsch G. Optimal spliced alignments of short sequence reads. Bioinformatics. 2008 Aug 15;24(16):i174-80. PubMed PMID:18689821.
2008
100
RNA-MATE
http://grimmond.imb.uq.edu.au/RNA-MATE/
1. RNA MATE is Mapping and Alignment Tool for Expression. 2. It is a tool used aligning RNA seq data from next generation sequencing platforms. 3. It aligns color space data.
Cloonan N, Xu Q, Faulkner GJ, Taylor DF, Tang DT, Kolle G, Grimmond SM. RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data. Bioinformatics. 2009 Oct 1;25(19):2615-6. Epub 2009 Jul 30. PubMed PMID: 19648138; PubMed Central PMCID: PMC2752615.
2009
100
RSEM - RNA Seq by Expectation Maximization
http://deweylab.biostat.wisc.edu/rsem/
1. It estimates quantity of RNA seq data and gene expression level. 2. It makes use of single-end and paired-end data.
Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics. 2010 Feb 15;26(4):493-500. Epub 2009 Dec 18. PubMed PMID: 20022975; PubMed Central PMCID: PMC2820677.
2010
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
SpliceMap
http://www.stanford.edu/group/wonglab/SpliceMap/
1. It is a tool used for identification of splice junction from RNA seq data. 2. Highly sensitive and specific. 3. It makes use of paired-end and long reads.
Au KF, Jiang H, Lin L, Xing Y, Wong WH. Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res. 2010 Aug;38(14):4570-8. Epub 2010 Apr 5. PubMed PMID: 20371516; PubMed Central PMCID: PMC2919714.
2010
100
SplitSeek
http://solidsoftwaretools.com/gf/project/splitseek/
1. It is for de novo splice junction prediction. 2. It can be used to detect splicing events and transcripts. 3. It can be also applied to detect indels.
Ameur A, Wetterbom A, Feuk L, Gyllensten U. Global and unbiased detection of splice junctions from RNA-seq data. Genome Biol. 2010;11(3):R34. Epub 2010 Mar 17. PubMed PMID: 20236510; PubMed Central PMCID: PMC2864574.
2010
100
Supersplat
http://supersplat.cgrb.oregonstate.edu/
1. It is a short read mapper which aligns RNA Seq data to the reference genome. 2. It performs gapped alignment to define the locations of potential introns. 3. It can detect potential splice junctions.
Bryant DW Jr, Shen R, Priest HD, Wong WK, Mockler TC. Supersplat--spliced RNA-seq alignment. Bioinformatics. 2010 Jun 15;26(12):1500-5. Epub 2010 Apr 21. PubMed PMID: 20410051; PubMed Central PMCID: PMC2881391.
2010
100
URL is not working as on 9th May 2012
TopHat
http://tophat.cbcb.umd.edu/index.html
1. It is a splice junction mapper which aligns RNA-Seq reads to large sized genomes using short read aligner bowtie. 2. It gives an output of splice junctions between exons from the mapping results.
Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009 May 1;25(9):1105-11. Epub 2009 Mar 16. PubMed PMID: 19289445; PubMed Central PMCID: PMC2672628.
2009
100
Trans-ABySS
http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss
1. Designed to analyze ABySS-assembled whole-genome shotgun transcriptome data. Contains scripts that will map assembled contigs to known transcripts, deduce novel splicing events such as exon-skipping, novel exons, intron retention, novel introns, and alternative splicing. 2. Also contains scripts that will extract potential SNVs, INDELs, and gene-fusion events from alignment data.
Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield YS, Newsome R, Chan SK, She R, Varhol R, Kamoh B, Prabhu AL, Tam A, Zhao Y, Moore RA, Hirst M, Marra MA, Jones SJ, Hoodless PA, Birol I. De novo assembly and analysis of RNA-seq data. Nat Methods. 2010 Nov;7(11):909-12. Epub 2010 Oct 10. PubMed PMID: 20935650.
2010
100
UnoSeq
http://unoseq.sourceforge.net/
1. It is a de novo transcriptome assembler. 2. It can assemble the reads, annotate contigs and analyze it.
Birzele F, Schaub J, Rust W, Clemens C, Baum P, Kaufmann H, Weith A, Schulz TW, Hildebrandt T. Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing. Nucleic Acids Res. 2010 Jul;38(12):3999-4010. Epub 2010 Mar 1. PubMed PMID: 20194116; PubMed Central PMCID: PMC2896516.
2010
100
 
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