abyss

de novo short read genome sequence assembler

brewmacoslinux

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Genome sequence assembler for short reads

ABYSSabyss-peAdjListDistanceEstOverlapPopBubblesSimpleGraphabyss-facabyss-filtergraph

Assemble paired-end reads with k-mer size of 64$ abyss-pe k=64 name=assembly in='reads_1.fastq reads_2.fastq'

Run assembly on multiple processors with coverage cutoff$ abyss-pe k=40 name=assembly np=8 c=2 in='sample_R1.fq sample_R2.fq'

Generate assembly statistics from contig file$ abyss-fac assembly-contigs.fa