Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
...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 /2kp2...1619 days ago
vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vt1619 days ago
Glia: a Graph/Smith-Waterman (partial order) aligner/realigner
...s to a set of known (or putative) variants in a VCF, both consuming and producing an ordered stream of BAM alignments. More at https://github.com/ekg/glia glia -f ~/human...1619 days ago
mutatrix: a population genome simulator which generates simulated genomes.
genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphisms More at https://github.com/ekg/mutatrix ./mutatrix -S sample -P test/ -p 2 -n 10 reference.fasta1619 days ago
Understanding your reads and mapping !
One of the best tutorial for beginners ... https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html1618 days ago
3D de novo assembly (3D DNA) pipeline
...nbsp;(Dudchenko et al., Science, 2017) see the original commit. For the detailed description of the merge section see https://github.com/theaidenlab/AGWG-merge.1614 days ago
alien_index : identify potential contaminants or horizontally transferred genes in transcriptomes.
identify potential contaminants or horizontally transferred genes in transcriptomes. algorithm is based on alogorithm described in the following: Gladyshev, Eugene A.,...1614 days ago
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Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
...it can be run on virtually any desktop or server. The software is available free of charge under the GNU General Public License from https://github.com/mourisl/Rcorrector/. Usa...1612 days ago
MEC: Contig Misassembly Correction
...reduce misassemblies effectively and result in quantitative improvements in scaffolding quality. MEC is publicly available for download at https://github.com/bioinfomaticsCSU/MEC.1612 days ago