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RAINBOWR: Reliable Association INference By Optimizing Weights with R (R package for SNP-set GWAS...
By Surabhi Chaudhary 2409 days agogithub.com - RAINBOWR(Reliable Association INference By Optimizing Weights with R) is a package to perform several types of GWAS as follows. Single-SNP GWAS with RGWAS.normal function SNP-set (or gene set) GWAS with RGWAS.multisnp function (which tests...vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
By Jit 2441 days agogenome.sph.umich.edu - 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/vtThe new corona variant has 23 mutations in all, which is unusually huge !
By Shruti Paniwala 2111 days agoThe new SARS-CoV-2 version, B.1.1.7, which was first seen in the third week of September in Kent and Greater London, has since spread to other locations in the UK.The Home Microbiome Project
By Abhimanyu Singh 4415 days agoThe Home Microbiome Project is an initiative aimed at uncovering the dynamic co-associations between people's bacteria and the bacteria found in their homes.The hope is that the data and project will show that routine monitoring of the microbial...REGEN: Ancestral Genome Reconstruction for Bacteria
By Rahul Nayak 3134 days agowww.mdpi.com - REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction is based on the...SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
By Jit 2853 days agolbbe.univ-lyon1.fr - The software package SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) with alignment coverage constraints. SiLiX adopts a graph-theoretical framework to...Trust But Verify: Sequencing Your Cell Lines Might Reveal an Uninvited Guest
By LEGE 487 days agoHigh-throughput sequencing has become indispensable in cell biology, enabling detailed insights into chromatin structure, gene expression, and regulatory dynamics. Yet, when faced with unexpectedly low mapping rates to the human genome,...When Thousands of Bacterial Genomes Become One Giant Map
By LEGE 38 days agoDeveloped by Jérôme Arnoux and colleagues, PANORAMA is a computational tool designed to explore bacterial pangenomes—the complete collection of genetic possibilities found across a species or group of related organisms. Instead of looking at every...CLARK: Fast, accurate and versatile sequence classification system
By Jit 2423 days agoclark.cs.ucr.edu - CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to...FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
By Jit 2441 days agobioinfo.ut.ee - FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the...
