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====== ABySS ====== | ====== 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. | ||
+ | |||
+ | [[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]] | ||
+ | |||
+ | |||
+ | =====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 |