ABYSS

NAME

ABYSS − assemble short reads into contigs

SYNOPSIS

ABYSS [OPTION]... FILE...

DESCRIPTION

Assemble all input files, FILE, which may be in FASTA, FASTQ, qseq, export, SRA, SAM or BAM format and may be compressed with gz, bz2 or xz and may be tarred.

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

AUTHOR

Written by Jared Simpson and Shaun Jackman.

REPORTING BUGS

Report bugs to <abyss-users AT bcgsc DOT ca>.

COPYRIGHT

Copyright 2015 Canada’s Michael Smith Genome Sciences Centre