Provided by: abyss_1.3.2-1_i386 bug


       abyss-pe - assemble reads into paired-end contigs


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


       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

       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.

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

              additional options to the single-end assembler, ABYSS

       cs     convert colour-space contigs  to  nucleotide  contigs  following

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

       -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.


       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.


   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'

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

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


       make(1), ABYSS(1)


       Written by Shaun Jackman.


       Report bugs to <>.


       Copyright 2011 Canada's Michael Smith Genome Science Centre