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DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from...
By Jit 2233 days agogithub.com - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation...pbmm2:A minimap2 frontend for PacBio native data formats
By BioStar 2209 days agogithub.com - pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for...Parliament2: Runs a combination of tools to generate structural variant calls on whole-genome...
By Jit 2108 days agogithub.com - Parliament2 identifies structural variants in a given sample relative to a reference genome. These structural variants cover large deletion events that are called as Deletions of a region, Insertions of a sequence into a region, Duplications of a...DADA2: Fast and accurate sample inference from amplicon data with single-nucleotide resolution
By Jit 1942 days agobenjjneb.github.io - The DADA2 tutorial goes through a typical workflow for paired end Illumina Miseq data: raw amplicon sequencing data is processed into the table of exact amplicon sequence variants (ASVs) present in each sample. The DADA2...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1471 days agogithub.com - This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes
By Abhi 1040 days agoorthovenn3.bioinfotoolkits.net - OrthoVenn3 is a powerful tool for comparative genomics analysis, used as a web server for full genome comparisons, annotation, and evolutionary analysis of orthologous clusters across multiple species. It has already been used by thousands of users...BioKit: a set of tools dedicated to bioinformatics, data visualisation
By Neel 627 days agobiokit.readthedocs.io - BioKit is a set of tools dedicated to bioinformatics, data visualisation (biokit.viz), access to online biological data (e.g. UniProt, NCBI thanks to bioservices). It also contains more advanced tools related to data analysis...BakRep (Denglish blend of Bakterien & Repository) simplifies access to this data
By Neel 206 days agobakrep.computational.bio - 2,438,386 bacterial genomes at your fingertips consistently processed & characterized, enriched with metadata, accessible via a flexible search engine. BakRep (Denglish blend of Bakterien & Repository) simplifies access to this data. It...GA4GH Data Working Group
By Jitendra Prajapati 3638 days agohttp://ga4gh.org/#/ - GA4GH Data Working Group Led by David Haussler (UCSC) and Richard Durbin (Sanger Institute), the Data Working Group (DWG) of the Global Alliance brings together the leading Genome Institutes and Centers with IT industry leaders to create global...Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
By Shruti Paniwala 2690 days agowww.well.ox.ac.uk - Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect...
