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--- contributors:team_4_page [2015/05/07 22:47]
JaredC created
+++ contributors:team_4_page [2015/05/08 02:16]
JaredC
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-====== ABySS ======
+======Team 4 | ABySS ======
+**A**ssembly **By** **S**hort **S**equences - a //de novo//, parallel, paired-end sequence assembler
+=====Team composition=====
+| Name | Email |
+| Jared Copher | jcopher@ucsc.edu |
+| Emilio Feal | efeal@ucsc.edu |
+| Sidra Hussain | sihussai@ucsc.edu |
+=====ABySS overview=====
+ABySS is published by Canada's Michael Smith Genome Sciences Centre, and was the first //de novo// assembler for large genomes recommended bu Illumina in [[http://www.illumina.com/Documents/products/technotes/technote_denovo_assembly_ecoli.pdf|this technical note]]  when using only their data. The ABySS team are active members on [[https://www.biostars.org/t/Abyss/|BioStars]] where they recommend all technical questions be asked.
+[[http://www.bcgsc.ca/platform/bioinfo/software/abyss | ABySS main site]]
+[[http://genome.cshlp.org/content/19/6/1117.full.pdf| ABySS paper]]
+[[https://github.com/bcgsc/abyss| ABySS manual and source code]]
+=====Installing ABySS=====
+ABySS source code was downloaded from Github
+<code>
+% lftpget https://github.com/bcgsc/abyss/archive/master.zip
+</code>
+ABySS needs to be configured with it's dependencies
+<code>
+% ./autogen.sh
+% ./configure --prefix=/campusdata/BME235\
+% --enable-maxk=96\  #must be a multiple of 32
+% --enable-dependency-tracking\
+% --with-boost=/campusdata/BME235/include/boost\
+% --with-mpi=/campusdata/BME235/include\
+% CC=gcc-4.9.2 CXX=g++-4.9.2\
+% CPPFLAGS=-I/campusdata/BME235/include/sparsehash
+</code>
+Then ABySS can be installed via the makefile
+<code>
+% make
+% make install
+</code>
+=====ABySS parameters=====
+Parameters of the driver script, abyss-pe
+  * 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 k-mer (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 [3]
+  * s: minimum unitig size required for building contigs (bp) [200]
+  * S: minimum contig size required for building scaffolds (bp) [s]
+  * t: minimum tip size (bp) [2k]
+  * v: use v=-v for verbose logging, v=-vv for extra verbose [disabled]
+Please see the abyss-pe manual page for more information on assembly parameters.
+Possibly, abyss-pe parameters can have same names as existing environment variables'. The parameters then cannot be used until the environment variables are unset. To detect such occasions, run the command:
+<code>
+abyss-pe env [options]
+</code>
+Above command will report all abyss-pe parameters that are set from various origins. However it will not operate ABySS programs.
+=====ABySS Programs=====
+abyss-pe is a driver script implemented as a Makefile. Any option of make may be used with abyss-pe. Particularly useful options are:
+<code>
+-C dir, --directory=dir
+</code>
+Change to the directory dir and store the results there.
+<code>
+-n, --dry-run
+</code>
+Print the commands that would be executed, but do not execute them.
+abyss-pe uses the following programs, which must be found in your PATH:
+  * ABYSS: de Bruijn graph assembler
+  * ABYSS-P: parallel (MPI) de Bruijn graph assembler
+  * AdjList: find overlapping sequences
+  * DistanceEst: estimate the distance between sequences
+  * MergeContigs: merge sequences
+  * MergePaths: merge overlapping paths
+  * Overlap: find overlapping sequences using paired-end reads
+  * PathConsensus: find a consensus sequence of ambiguous paths
+  * PathOverlap: find overlapping paths
+  * PopBubbles: remove bubbles from the sequence overlap graph
+  * SimpleGraph: find paths through the overlap graph
+  * abyss-fac: calculate assembly contiguity statistics
+  * 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-scaffold: scaffold contigs using distance estimates
+  * abyss-todot: convert graph formats and merge graphs
+=====ABySS pipeline=====
+{{ :bioinformatic_tools:abysspipeline.png?nolink |}}

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