Jit
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RapClust: Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence...
By Rahul Nayak 2242 days agogithub.com - RapClust is a tool for clustering contigs from de novo transcriptome assemblies. RapClust is designed to be run downstream of the Sailfish or Salmon tools for rapid transcript-level quantification. Specifically,...Cleaner BLAST Databases for More Accurate Results
By LEGE 215 days agoRemoving contaminated sequences using NCBI quality assurance toolsThe Home Microbiome Project
By Abhimanyu Singh 3735 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 2454 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 2173 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...Snippy: Rapid haploid variant calling and core SNP phylogeny
By Neel 2296 days agogithub.com - Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is...Rules for Pango Lineage !
By Abhi 1075 days agowww.pango.network - All the rules to classify a Lineage ! https://www.pango.network/the-pango-nomenclature-system/statement-of-nomenclature-rules/CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
By Jit 1650 days agogithub.com - Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by...Understanding DUMP files from NCBI Taxonomy database !
By Shruti Paniwala 862 days agoTaxonomy database !Dengue Lineages !
By LEGE 99 days agodengue-lineages.org - Our dengue virus lineage system splits up the current genotypes into major and minor lineages to provide additional spatiotemporal resolution and a common language to discuss important genomic diversity. A full description of the lineage system can...
