SIMPLE SOLUTIONS

ABYSS-PE(1) - man page online | user commands

Assemble reads into contigs.

Chapter
2015-May
abyss-pe(1)                               User Commands                               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}-scaf‐ folds.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 exam‐ ple of usage. pe list of paired-end libraries that will be used only for merging unitigs into con‐ tigs 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 assem‐ bled 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 con‐ tain 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 con‐ tain 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 con‐ tain 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 con‐ tain 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/plat‐ form/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 envi‐ ronment 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 <@googlegroups.com>.
abyss-pe (ABySS) 1.9.0 2015-May abyss-pe(1)
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refer to ABYSS(1) | make(1)