lecture_notes:04-20-2015
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lecture_notes:04-20-2015 [2015/04/21 09:24] gepoliano created |
lecture_notes:04-20-2015 [2015/04/25 02:55] calef [Basic features] |
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| ======Team 1 report: assembly with Meraculous====== | ======Team 1 report: assembly with Meraculous====== | ||
| =====Basic features===== | =====Basic features===== | ||
| - | Published by the US Department of energy. Meraculous was initially designed for haploid assembly, but currently supports diploid assembly as well. The advantages of this assembler include multi-threaded and parallelized computation, absence of error-correction for faster processing, paired-end short reads compatibility (e.g., Illumina), efficient and conservative traversal of subgraphs of the de Bruijn graph, selection of kmer set, production of a set of maximal linear sub-paths of the de Bruijn graph, alignment of reads to assembly in order to identify useful read-pair information and closure of gaps. Meraculous has been used to assemble //Pichia stipitis// genome, producing 15.4 Mb genome, 75 bp paired reads with 425x coverage. As a result, 95% of the genome was covered and an N50 = 101 kb was obtained. | + | Published by the Joint Genome Institute, part of the US Department of Energy. Meraculous was initially designed for haploid assembly, but currently supports diploid assembly as well. The advantages of this assembler include multi-threaded and parallelized computation, absence of error-correction for faster processing, paired-end short reads compatibility (e.g., Illumina), efficient and conservative traversal of subgraphs of the de Bruijn graph, selection of kmer set, production of a set of maximal linear sub-paths of the de Bruijn graph, and alignment of reads to assembly in order to identify useful read-pair information and closure of gaps. Meraculous has been used to assemble the //Pichia stipitis// genome, a 15.4 Mb genome, using 75 bp paired reads with 425x coverage. The resulting assembly covered 95% of the genome and had an N50 of 101 kb. |
| =====Meraculous algorithm===== | =====Meraculous algorithm===== | ||
lecture_notes/04-20-2015.txt · Last modified: 2015/04/25 03:07 by calef
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