abyss-pe(1)

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