Provided by: abyss_1.9.0-1build1_amd64 bug

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.

       long   list of long sequence libraries that will be used for rescaffolding.  long sequence
              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 a k-mer (when K is not set) or the span of a k-mer pair (when K is set)

       K      size of a single k-mer in a k-mer pair (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 when trimming [3]
              Trim bases from the ends of reads whose quality is less q.

       Q      minimum base quality [0]
              Mask all bases of reads whose quality is less than Q as `N'.

       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]

       SS     SS=--SS to assemble in strand-specific mode
              Requires that all libraries are strand-specific RNA-Seq  libraries.   Assumes  that
              the first read in a read pair is reveresed WRT the transcripts sequenced.

       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].
              Permitted  values  are:  map, kaligner, bwa, bwasw, bowtie, bowtie2, dida.  See the
              DIDA section below for further info on the dida option.

       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.  SAM  file  will  only
              contain  reads  mapping to different contigs, and the read ID, sequence and quality
              strings will be replaced with '*' characters.

       pe-bam Map paired-end reads to the unitigs and output a  BAM  file.  BAM  file  will  only
              contain  reads  mapping to different contigs, and the read ID, sequence and quality
              strings will be replaced with '*' characters.

       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.  SAM  file  will  only
              contain  reads  mapping to different contigs, and the read ID, sequence and quality
              strings will be replaced with '*' characters.

       mp-bam Map mate-pair reads to the contigs and output  a  BAM  file.  BAM  file  will  only
              contain  reads  mapping to different contigs, and the read ID, sequence and quality
              strings will be replaced with '*' characters.

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

       scaffolds
              Assemble scaffolds.

       scaffolds-dot
              Output the scaffold overlap graph.

       scaftigs
              Break scaffolds and generate AGP file.

       long-scaffs
              Rescaffold using RNA-Seq assembled contigs.

       long-scaffs-dot
              Output the RNA 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.

DIDA

       ABySS supports the use of DIDA (Distributed Indexing Dispatched Alignment),  an  MPI-based
       alignment  framework  for  computing  sequence alignments across multiple machines. To use
       DIDA     with     ABySS,     first      download      and      install      DIDA      from
       http://www.bcgsc.ca/platform/bioinfo/software/dida,  then  specify  `dida` as the value of
       the aligner parameter to abyss-pe.

   DIDA-related abyss-pe parameters
       DIDA_MPIRUN
              The `mpirun` command used to run DIDA jobs.

       DIDA_RUN_OPTIONS
              Runtime options such as number of threads per MPI rank and values  for  environment
              variables  (e.g.  PATH,  LD_LIBRARY_PATH).   Run  `abyss-dida --help` for a list of
              available options.

       DIDA_OPTIONS
              Options that are passed directly to the DIDA binary. For example, this can be  used
              to control the minimum alignment length threshold.  Run `dida-wrapper --help` for a
              list of available options.

   MPI COMPATIBILITY
       Due to its use of multi-threading, DIDA has known deadlocking issues with OpenMPI.   Using
       the  MPICH MPI library is strongly recommmended when running assemblies with DIDA. Testing
       was done with MPICH 3.1.3, compiled with --enable-threads=funneled.

   EXAMPLE
       The recommended runtime configuration for DIDA is 1 MPI rank per machine and 1 thread  per
       CPU core. For example, to run an assembly across 3 cluster nodes with 12 cores each, do:

            abyss-pe      k=64      name=ecoli      in='reads1.fa     reads2.fa'     aligner=dida
       DIDA_RUN_OPTIONS='-j12' DIDA_MPIRUN='mpirun -np 3 -ppn 1 -bind-to board'

       This example uses the MPICH command line options for `mpirun`.  Here,  `-np  3`  indicates
       the  number  of  MPI  ranks,  `-ppn  1`  indicates the number of MPI ranks per "node", and
       `-bind-to board` defines a "node" to be a motherboard (i.e. a full machine).

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'

   Including RNA-Seq assemblies
        abyss-pe k=64 name=ecoli lib=pe1 mp=mp1 long=long1 \
            pe1='pe1_1.fa pe1_2.fa' mp1='mp1_1.fa mp1_2.fa' \
            long1=long1.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 2015 Canada's Michael Smith Genome Sciences Centre