ABYSS(1) - man page online | user commands
Assemble short reads into contigs.
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 dis‐ tance 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 REPORTING BUGS Report bugs to <@bcgsc.ca>. COPYRIGHT Copyright 2015 Canada's Michael Smith Genome Sciences CentreABYSS (ABySS) 1.9.0 2015-May ABYSS(1)
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