NAME

       abyss-pe - assemble reads into contigs

SYNOPSIS

       abyss-pe [OPTION]...  [PARAMETER=VALUE]...  [MAKE_TARGET]...

DESCRIPTION

       Assemble  the reads of the input files into contigs. The reads 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.

       abyss-pe is a Makefile script. Any options of make may also be used with abyss-pe.

   Parameters of abyss-pe
       name, JOB_NAME
              The name of this assembly. The resulting scaffolds will be stored in ${name}-scaffolds.fa.

       in     input files. Use this variable when assembling data from a single library.

       lib    a quoted list of whitespace-separated paired-end library names. Use this varible  when  assembling
              data  from  multiple  paired-end  libraries.  For each library name in lib, the user must define a
              variable on the command line with the same name, which indicates the read files for that  library.
              See EXAMPLES below for a concrete example of usage.

       pe     list  of paired-end libraries that will be used only for merging unitigs into contigs and will not
              contribute toward the consensus sequence.

       mp     list of mate-pair libraries that will  be  used  for  scaffolding.   Mate-pair  libraries  do  not
              contribute toward the consensus sequence.

       se     files containing single-end reads

       a      maximum number of branches of a bubble [2]

       b      maximum length of a bubble (bp) [10000]

       c      minimum mean k-mer coverage of a unitig [sqrt(median)]

       d      allowable error of a distance estimate (bp) [6]

       e      minimum erosion k-mer coverage [sqrt(median)]

       E      minimum erosion k-mer coverage per strand [1]

       j      number of threads [2]

       k      size of k-mer (bp)

       l      minimum alignment length of a read (bp) [k]

       m      minimum overlap of two unitigs (bp) [30]

       n      minimum number of pairs required for building contigs [10]

       N      minimum number of pairs required for building scaffolds [n]

       p      minimum sequence identity of a bubble [0.9]

       q      minimum base quality [3]
              Trim bases from the ends of reads whose quality is less q.

       s      minimum unitig size required for building contigs (bp) [200]
              The  seed  length  should be at least twice the value of k. If more sequence is assembled than the
              expected genome size, try increasing s.

       S      minimum contig size required for building scaffolds (bp) [s]

       t      minimum tip size (bp) [2k]

       v      v=-v to enable verbose logging

       np, NSLOTS
              the number of processes of an MPI assembly

       mpirun the path to mpirun

       aligner
              the program to use to align the reads to the contigs [map]
              map, kaligner, bwa, bwasw, bowtie or bowtie2

       cs     convert colour-space contigs to nucleotide contigs following assembly

   Options of make
       -n, --dry-run
              Print the commands that would be executed, but do not execute them.

   Make targets for abyss-pe
       default
              Equivalent to `scaffolds scaffolds-dot stats'.

       unitigs
              Assemble unitigs.

       unitigs-dot
              Output the unitig overlap graph.

       pe-sam Map paired-end reads to the unitigs and output a SAM file.

       pe-bam Map paired-end reads to the unitigs and output a BAM file.

       pe-index
              Generate an index of the unitigs used by abyss-map.

       contigs
              Assemble contigs.

       contigs-dot
              Output the contig overlap graph.

       mp-sam Map mate-pair reads to the contigs and output a SAM file.

       mp-bam Map mate-pair reads to the contigs and output a BAM file.

       mp-index
              Generate an index of the contigs used by abyss-map.

       scaffolds
              Assemble scaffolds.

       scaffolds-dot
              Output the scaffold overlap graph.

       stats  Display assembly contiguity statistics.

       clean  Remove intermediate files.

       version
              Display the version of abyss-pe.

       versions
              Display the versions of all programs used by abyss-pe.

       help   Display a helpful message.

ENVIRONMENT VARIABLES

       Any parameter that may be specified on the command line may also be specified in an environment variable.

       PATH   must contain the directory where the ABySS executables are installed.  Use `abyss-pe versions`  to
              check that PATH is configured correctly.

       TMPDIR specifies a directory to use for temporary files

   Scheduler integration
       ABySS integrates well with cluster job schedulers, such as:
        * SGE (Sun Grid Engine)
        * Portable Batch System (PBS)
        * Load Sharing Facility (LSF)
        * IBM LoadLeveler

       The  SGE  environment  variables  JOB_NAME,  SGE_TASK_ID and NSLOTS may be used to specify the parameters
       name, k and np, respectively, and similarly for other schedulers.

EXAMPLES

   One paired-end library
        abyss-pe k=64 name=ecoli in='reads1.fa reads2.fa'

   Multiple paired-end libraries
        abyss-pe k=64 name=ecoli lib='lib1 lib2' \
            lib1='lib1_1.fa lib1_2.fa' lib2='lib2_1.fa lib2_2.fa' \
            se='se1.fa se2.fa'

   Paired-end and mate-pair libraries
        abyss-pe k=64 name=ecoli lib='pe1 pe2' mp='mp1 mp2' \
            pe1='pe1_1.fa pe1_2.fa' pe2='pe2_1.fa pe2_2.fa' \
            mp1='mp1_1.fa mp1_2.fa' mp2='mp2_1.fa mp2_2.fa' \
            se='se1.fa se2.fa'

   MPI
        abyss-pe np=8 k=64 name=ecoli in='reads1.fa reads2.fa'

   SGE
        qsub -N ecoli -t 64 -pe openmpi 8 \
            abyss-pe n=10 in='reads1.fa reads2.fa'

SEE ALSO

       make(1), ABYSS(1)

AUTHOR

       Written by Shaun Jackman.

REPORTING BUGS

       Report bugs to <abyss-users@googlegroups.com>.

COPYRIGHT

       Copyright 2013 Canada's Michael Smith Genome Science Centre