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.

       --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

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