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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, ex-
       port, 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

ABYSS (ABySS) 2.2.4		   2015-May			      ABYSS(1)

NAME | SYNOPSIS | DESCRIPTION | AUTHOR | REPORTING BUGS | COPYRIGHT

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