Abyss-tofastq converts to FASTQ format. The input format may be FASTA, FASTQ, qseq, export, SAM or BAM format and compressed with gz, bz2 or xz and may be tarred.
Parent program: abyss
ABySS is a de novo sequencing assembler developed for short reads of large genomes. It has novel scaffolding algorithm capable of assembling very large genomes including human genomes (>3.5 billion paired-end reads). ABySS algorithm eliminates ambiguities in the scaffold graph and identifies contigs that are assembled into scaffolds.The assembly runs in three stages: assemble contigs without paired-end information, align the paired-end reads to the initial assembly, and merge contigs joined by paired-end information.