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--- contributors:team_4_page [2015/05/08 02:19]
JaredC
+++ contributors:team_4_page [2015/05/11 08:47]
emfeal [Running ABySS]
@@ Line 20: / Line 20: @@
 [[https://github.com/bcgsc/abyss| ABySS manual and source code]]
+=====General notes=====
+  - ABySS can run in serial mode, but that isn't too useful for such a large genome.
+  - The documentation recommends creating assemblies with several values of k and selecting the "best" one.
+  - The program involves its own error correction.
 =====Installing ABySS=====
@@ Line 74: / Line 79: @@
 Above command will report all abyss-pe parameters that are set from various origins. However it will not operate ABySS programs.
-=====ABySS Programs=====
+=====Running ABySS=====
+Running an assembly on the campusrocks cluster, which runs on SGE, requires the use of the qsub command.  The use of a shell script allows a convenient and concise way to wrap useful qsub options, environmental variable manipulations, and the executable (abyss-pe) itself in a single script. An example script which runs
+the parallel-version of ABySS on the cluster is shown below.
+<code>
+#!/bin/sh
+#$ -N team4
+#$ -cwd
+#$ -j y
+#$ -pe mpi 10
+#$ -S /bin/bash
+#$ -V
+#$ -l mem_free=15g
+ABYSSRUNDIR=/campusdata/BME235/bin
+export PATH=$PATH:/opt/openmpi/bin:/campusdata/BME235/bin/
+export LD_LIBRARY_PATH=/opt/openmpi/lib/:$LD_LIBRARY_PATH
+ABYSSRUN=$ABYSSRUNDIR/abyss-pe
+$ABYSSRUN np=10 k=21 name=ecoli in='/campusdata/BME235/programs/abyss-1.5.2/JARED/test-data/reads1.fastq /campusdata/BME235/programs/abyss-1.5.2/JARED/test-data/reads2.fastq'
+</code>
+Note that the parallel version of ABySS requires two things in particular:
+**(1)** the use of a parallel environment which can be selected using a qsub option.  The parallel environment option in the script above:
+<code>
+#$ -pe mpi 10
+</code>
+The //mpi// designates the choice of a parallel environment that is installed on the system and the 10 indicates the number of processes over which to run the job. To see which PE's are installed on the system, use the command:
+<code>
+qconf -spl
+</code>
+**(2)**the //np// option of abyss-pe. The number of processes here must reflect the number included in the parallel
+environment option.
 abyss-pe is a driver script implemented as a Makefile. Any option of make may be used with abyss-pe. Particularly useful options are:
@@ Line 86: / Line 120: @@
 Print the commands that would be executed, but do not execute them.
+===Commands of 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.
+===Programs in pipeline===
 abyss-pe uses the following programs, which must be found in your PATH:
@@ Line 102: / Line 157: @@
   * abyss-filtergraph: remove shim contigs from the overlap graph
   * abyss-fixmate: fill the paired-end fields of SAM alignments
-  * abyss-map: map reads to a reference sequence
+  * abyss-map: map reads to a reference sequence (BW transform)
   * abyss-scaffold: scaffold contigs using distance estimates
   * abyss-todot: convert graph formats and merge graphs
+New to Version 1.3.5 (Mar 05, 2013)
+  * abyss-mergepairs: Merges overlapping read pairs.
+  * abyss-layout: Layout contigs using the sequence overlap graph.
+  * abyss-samtobreak: Calculate contig and scaffold contiguity and correctness metrics.
+New to Version 1.5.2 (Jul 10, 2014)
+  * konnector: fill the gaps between paired-end reads by building a Bloom filter de Bruijn graph and searching for paths between paired-end reads within the graph
+  * abyss-bloom: construct reusable bloom filter files for input to Konnector
 =====ABySS pipeline=====
@@ Line 110: / Line 172: @@
 {{ :bioinformatic_tools:abysspipeline.png?nolink |}}
+=====Test run=====
+This run was done using version 1.5.2. The assembly used k=59, 10 processes, and requested mem_free=15g from qsub. The assembly was done using the SW018 and SW019 libraries only. Specifically, the files used were:
+  * /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep/SW018_S1_L007_R1_001_trimmed.fastq.gz
+  * /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep/SW018_S1_L007_R2_001_trimmed.fastq.gz
+  * /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep/SW019_S1_L001_R1_001_trimmed.fastq.gz
+  * /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep/SW019_S1_L001_R2_001_trimmed.fastq.gz
+  * /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep/SW019_S2_L008_R1_001_trimmed.fastq.gz
+  * /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep/SW019_S2_L008_R2_001_trimmed.fastq.gz
+The files had adapters trimmed using SeqPrep (see the data pages for more details). SW019_S1 and SW019_S2 were treated as two separate libraries.
+The output and log files for this assembly are in /campusdata/BME235/S15_assemblies/abyss/sidra/test_run/singleK.
+====Results====
+Note: the N50, etc., stats only include contigs >= 500 bp (I believe the rest are discarded).
+There are 10.23 * 10^6 contigs. The N50 contig size is 2,669. The number of contigs of at least N50 (n:N50) is 174,507. The maximum contig size is 31,605, and the total number of bp (in contigs >= 500 bp) is 1.557 * 10^9.
+Here are the stats summarized for the contigs and also for scaffolds and unitigs. n:500 is the number of contigs/unitigs/scaffolds at least as long as 500 bp. sum is the number of bases in all the contigs/unitigs/scaffolds at least as long as 500 bp combined.
+| n | n:500 | n:N50 | min | N80 | N50 | N20 | E-size | max | sum | name |
+| 11.95e6 | 993409 | 247109 | 500 | 962  | 1795 | 3327 | 2296 | 30520 | 1.456e9 | slug-unitigs.fa |
+| 10.23e6 | 785054 | 174507 | 500 | 1320 | 2669 | 5079 | 3433 | 31605 | 1.557e9 | slug-contigs.fa |
+| 10.11e6 | 711022 | 153036 | 500 | 1490 | 3063 | 5870 | 3945 | 37466 | 1.573e9 | slug-scaffolds.fa |
+====Notes====
+The success of this run means we are probably ready to do a run with all the data (not including the mate-pair data, that can be used for scaffolding later). For that run, the different trimmed files for each library should be concatenated, so that the run involves only the actual number of libraries we had (I believe 4?). It should also use many more than 10 processes.

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