<![CDATA[BOL: Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search]]> https://bioinformaticsonline.com/bookmarks/view/40703/%CF%80-cyc-a-reference-free-snp-discovery-application-using-parallel-graph-search? https://bioinformaticsonline.com/bookmarks/view/40703/%CF%80-cyc-a-reference-free-snp-discovery-application-using-parallel-graph-search Tue, 28 Jan 2020 03:34:23 -0600 https://bioinformaticsonline.com/bookmarks/view/40703/%CF%80-cyc-a-reference-free-snp-discovery-application-using-parallel-graph-search <![CDATA[Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search]]> Reference free SNP search for comparative population genomics: multiple samples run simultanously. **experimental phase, compiles and runs with OpenMPI-1.8.8 with Intel Compiler only

Cycles enumeration (aka Bubbles) as part of de novo de bruijn graphs assembly using colours can be unpractical for large error prone genomes which makes the assembly process produce an excessive number of false positive cycles.  Our solution is to search the graph in multicores shared memory parallel mode using graph decomposition then use filtering method to generate good quality SNPs.

https://arxiv.org/abs/1809.06700

https://github.com/redayounsi/2KP2P

/2kp2omp/bin/main_2kp2_K63_C2 -i fastq_files.txt -o fungus_bub.fasta -r stat_fungus.txt -c cov_fungus_hash.txt -k 63 -h 20 -b 100 -g 600 -l 100 -f 16 -t 5.0 -x 1 -v 0 -p 1 -y 1 -u 1

 

Address of the bookmark: https://github.com/redayounsi/2KP2P

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