Provided by: abyss_1.3.6-1build1_amd64 
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