Provided by: abyss_1.3.2-1_amd64 bug

NAME

       abyss-pe - assemble reads into paired-end contigs

SYNOPSIS

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

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  contigs  will  be  stored  in
              ${name}-contigs.fa.

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

       lib    list of paired-end libraries. Use this varible when assembling data  from  multiple
              fragment  libraries.  For  each  library in lib, a variable with the same name must
              specify the files containing those reads.

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

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

       se     files containing single-end reads

       k, SGE_TASK_ID
              k-mer size

       q      quality threshold. Trim bases from the ends of reads whose quality is less than the
              threshold. (default: 3)

       e      erosion k-mer coverage threshold

       c      mean k-mer coverage threshold

       b      pop bubbles shorter than N bp (default: 10000).

       p      pop bubbles with identity at least p (default: 0.9)

       n      minimum number of pairs (default: 10). The optimal value for this parameter depends
              on coverage, but 10 is a reasonable default.

       s      minimum length of a seed contig in bp (default: 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.

       d      acceptable error in bp of a distance estimate (default: 6).

       np, NSLOTS
              the number of processes of an MPI assembly

       mpirun the path to mpirun

       j      the number of threads to use (default: 2). If np is specified, the default  is  the
              value of np.

       aligner
              specify the program to use to align reads to contigs:
              kaligner, map, bwa, bwasw or bowtie. The default is kaligner.

       ABYSS_OPTIONS
              additional options to the single-end assembler, ABYSS

       cs     convert colour-space contigs to nucleotide contigs following assembly

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

       -j jobs
              Specifies  the  number  of jobs to run simultaneously. For abyss-pe, this parameter
              should be set to the number of libraries being assembled.

ENVIRONMENT VARIABLES

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

       PATH   should contain the directory where ABYSS was installed.

       TMPDIR specifies a directory to use for temporary files.

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

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 2011 Canada's Michael Smith Genome Science Centre