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Suggested Readings
A compilation and categorization of next-generation sequencing resources

ABySS - Assembly By Short Sequences

Tool nameABySS - Assembly By Short Sequences
Important features1. It is a de novo, parallel, paired-end sequence assembler. 2. It can be run in paired-end mode. ABySS transfers the sequence reads into binary format to save the computational space. It can handle read errors, perform well for large genome assembly.
CitationsSimpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. ABySS: a parallel assembler for short read sequence data. Genome Res. 2009 Jun;19(6):1117-23. Epub 2009 Feb 27. PubMed PMID: 19251739; PubMed Central PMCID: PMC2694472.
Year of publication2009
Rank by usage frequency100
FunctionDe novo assembler
CategoryFree, Downloadable
Input file formatFASTA and FASTQ, QSEQ, SAM, BAM
Output file formatFASTA
Operating systemLinux, Mac OS X
Operating languageC++
PlatformRoche 454, Illumina/Solexa, ABI SOLiD
Maintained byShaun Jackman
Downloadable file format
Submission file format

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