NAME

SYNOPSIS

DESCRIPTION

Users wishing to run a full assembly with ABySS are recommended to use abyss-pe as their entry point rather than the ABYSS program. abyss-pe is a Makefile that coordinates many of the ABySS tools (including ABYSS) in order to run the full ABySS assembly pipeline. abyss-pe is capable of doing many things that ABYSS is not, such as leveraging the distance information provided by paired end reads and mate pair reads.

--chastity

discard unchaste reads [default]

--no-chastity

do not discard unchaste reads

--trim-masked

trim masked bases from the ends of reads [default]

--no-trim-masked

do not trim masked bases from the ends of reads

-q, --trim-quality=THRESHOLD

trim bases from the ends of reads whose quality is less than the threshold

-Q, --mask-quality=THRESHOLD

mask all bases in reads whose quality is less than the threshold

--standard-quality

zero quality is `!' (33)
default for FASTQ and SAM files

--illumina-quality

zero quality is `@' (64)
default for qseq and export files

-o, --out=FILE

write the contigs to FILE

-k, --kmer=KMER_SIZE

k-mer size

-t, --trim-length=TRIM_LENGTH

maximum length of dangling edges to trim

-c, --coverage=COVERAGE

remove contigs with mean k-mer coverage less than this threshold

-b, --bubbles=N

pop bubbles shorter than N bp (default: 3*k).

-b0, --no-bubbles

do not pop bubbles

-e, --erode=COVERAGE

erode bases at the ends of blunt contigs with coverage less than this threshold

-E, --erode-strand=COVERAGE

erode bases at the ends of blunt contigs with coverage less than this threshold on either strand

--coverage-hist=FILE

record the k-mer coverage histogram in FILE

-g, --graph=FILE

generate a graph in dot format

-s, --snp=FILE

record popped bubbles in FILE

-v, --verbose

display verbose output

--help

display this help and exit

--version

output version information and exit

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