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A compilation and categorization of next-generation sequencing resources

ALLPATHS

Tool nameALLPATHS
URLhttp://www.broadinstitute.org/science/programs/genome-biology/computational-rd/computational-research-and-development
Important features1. ALLPATHS requires paired-end reads. It can use unpaired reads to improve error correction. 2. ALLPATHS assemblies are not necessarily linear, but instead are presented in the form of a graph. (a) finding all paths across a given read pair, i.e., all sequences from one read to the other that are covered by other reads, and (b) localization, a way of using pairs to isolate small regions of the genome and assemble them independently.
CitationsButler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res. 2008 May;18(5):810-20. Epub 2008 Mar 13. PubMed PMID: 18340039; PubMed Central PMCID: PMC2336810.
Year of publication2008
Rank by usage frequency100
Comments
FunctionDe novo assembler
CategoryFree, Downloadable
License
Status
Input file formatFASTA, .qual
Output file format.dot, FASTA, .ps
Operating system Linux/Unix 32/64 bit
Operating languageC++
PlatformIllumina/Solexa
Maintained byComputational Research and Development Group,Cambridge
Downloadable file format
Submission file format

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