NOTE: Univa's fork of SGE/OGE reguires the qsub option '-b' to be set to yes. This lets qsub know that the command (abyss-pe) is a binary file. Without this option qsub tries to run abyss-pe as a script file.
== See also ==
Try `abyss --help' for more information on command line options, or
see the manual page in the file `ABYSS.1'.
Please refer to the mpirun manual page for information on configuring
parallel jobs.
Written by Jared Simpson and Shaun Jackman.
Subscribe to the users' mailing list at
http://www.bcgsc.ca/mailman/listinfo/abyss-users
Contact the users' mailing list at <abyss-users@bcgsc.ca>
or the authors directly at <abyss@bcgsc.ca>.
= Usage =
Usage: ABYSS [OPTION]... FILE...
Assemble the input files, FILE, which may be in FASTA, FASTQ,
qseq or export format and compressed with gz, bz2 or xz.
--chastity discard unchaste reads [default]
for qseq- and export-formatted files only
--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
-o, --out=FILE write the contigs to FILE
the default is contigs.fa
-k, --kmer=KMER_SIZE k-mer size
-l, --read-length=READ_LENGTH read length
-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 maximum number of bubble-popping rounds
-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. default=1
--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
Report bugs to <abyss-users@bcgsc.ca>.
= MAN =
<pre>
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 (.fa) format or FASTQ format (.fastq) and may be
compressed with gz, bz2 or xz.
--chastity
discard unchaste reads [default] for qseq and export files only
--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
--standard-quality
zero quality is ‘!’ (33) default for FASTQ 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
-l, --read-length=READ_LENGTH
read length
-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
maximum number of bubble-popping rounds
-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.
default=1
--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@bcgsc.ca>.
COPYRIGHT
Copyright 2009 Canada’s Michael Smith Genome Science Centre
ABYSS (ABySS) 1.1.0 2009-Nov ABYSS(1)
</pre>
{{Links}}
{{References}}
{{Link box}}
