abyss-pe - Online in the Cloud

PROGRAM:

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'

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