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ABYSS(1) User Commands ABYSS(1)

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.

discard unchaste reads [default]
do not discard unchaste reads
trim masked bases from the ends of reads [default]
do not trim masked bases from the ends of reads
trim bases from the ends of reads whose quality is less than the threshold
mask all bases in reads whose quality is less than the threshold
zero quality is `!' (33)
default for FASTQ and SAM files
zero quality is `@' (64)
default for qseq and export files
write the contigs to FILE
k-mer size
maximum length of dangling edges to trim
remove contigs with mean k-mer coverage less than this threshold
pop bubbles shorter than N bp (default: 3*k).
do not pop bubbles
erode bases at the ends of blunt contigs with coverage less than this threshold
erode bases at the ends of blunt contigs with coverage less than this threshold on either strand
record the k-mer coverage histogram in FILE
generate a graph in dot format
record popped bubbles in FILE
display verbose output
display this help and exit
output version information and exit

AUTHOR

Written by Jared Simpson and Shaun Jackman.

REPORTING BUGS

Report bugs to <abyss-users@bcgsc.ca>.

COPYRIGHT

Copyright 2015 Canada's Michael Smith Genome Sciences Centre

2015-May ABYSS (ABySS) 2.3.1