SYNOPSISABYSS [OPTION]... FILE...
DESCRIPTIONAssemble 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
- -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
zero quality is `!' (33)
default for FASTQ and SAM files
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
- 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
- display this help and exit
- output version information and exit
AUTHORWritten by Jared Simpson and Shaun Jackman.
REPORTING BUGSReport bugs to <[email protected]>.
COPYRIGHTCopyright 2015 Canada's Michael Smith Genome Sciences Centre