ALLPATHS | Tool name | ALLPATHS |
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| URL | http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/computational-research-and-development |
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| Important features | 1. 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. |
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| Citations | Butler 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. |
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| Year of publication | 2008 |
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| Rank by usage frequency | 100 |
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| Comments | |
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| Function | De novo assembler |
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| Category | Free, Downloadable |
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| License | |
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| Status | |
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| Input file format | FASTA, .qual |
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| Output file format | .dot, FASTA, .ps |
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| Operating system |
Linux/Unix 32/64 bit |
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| Operating language | C++ |
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| Platform | Illumina/Solexa |
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| Maintained by | Computational Research and Development Group,Cambridge
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| Downloadable file format | |
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| Submission file format | |
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