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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  com-
       pressed 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 sin-
	      gle 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  con-
	      crete 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  consen-
	      sus sequence.

       mp     list  of	mate-pair libraries that will be used for scaffolding.
	      Mate-pair	libraries do not contribute toward the	consensus  se-
	      quence.

       long   list  of	long  sequence libraries that will be used for rescaf-
	      folding.	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 in-
	      creasing 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 li-
	      braries.	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 as-
	      sembly

   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	Align-
       ment), an MPI-based alignment framework for computing  sequence	align-
       ments  across multiple machines.	To use DIDA with ABySS,	first download
       and  install   DIDA   from   http://www.bcgsc.ca/platform/bioinfo/soft-
       ware/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  val-
	      ues 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	 exam-
	      ple,  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, com-
       piled with --enable-threads=funneled.

   EXAMPLE
       The recommended runtime configuration for DIDA is 1 MPI	rank  per  ma-
       chine 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 num-
       ber 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  in-
	      stalled.	 Use `abyss-pe versions` to check that PATH is config-
	      ured 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 simi-
       larly 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 <abyss-users@googlegroups.com>.

COPYRIGHT
       Copyright 2015 Canada's Michael Smith Genome Sciences Centre

abyss-pe (ABySS) 2.2.4		   2015-May			   abyss-pe(1)

NAME | SYNOPSIS | DESCRIPTION | DIDA | ENVIRONMENT VARIABLES | EXAMPLES | SEE ALSO | AUTHOR | REPORTING BUGS | COPYRIGHT

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