abyss-pe1

Assemble reads into contigs

Usage

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

Overview

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 variable 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) [""]
abyss-pe has two bubble popping stages. The default limits are 3*k bp for ABYSS and 10000 bp for PopBubbles.

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 [round(sqrt(median))]

E: minimum erosion k-mer coverage per strand [1 if sqrt(median) > 2 else 0]

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) [40]

m: minimum overlap of two unitigs (bp) [k-1]

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) [1000]
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) [1000-10000]

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 reversed WRT the transcripts sequenced.

t: maximum length of blunt contigs to trim [k]

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 recommended 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

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'

Releases

4 releases since Debian 9 (Stretch); the text changed 3 times.