ABYSS - assemble short reads into contigs
ABYSS [
OPTION]...
FILE...
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
Written by Jared Simpson and Shaun Jackman.
Report bugs to <
[email protected]>.
Copyright 2014 Canada's Michael Smith Genome Sciences Centre