BioStar
Bioinformatician
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The Tree That Learned to Read Genomes
By BioStar 27 days agoA recent study by Webster and Chapman introduces Buscogeny, an open-source bioinformatics pipeline designed to make this process easier. The tool uses BUSCO (Benchmarking Universal Single-Copy Orthologs), which identifies conserved genes that are...Understanding pango networks !
By Abhi 1818 days agowww.pango.network - In the vast majority of instances it is expected that Pango lineage names and designations will conform to the following rules. These rules also act as guidelines for the decisions made by the Lineage Designation...Rules for Pango Lineage !
By Abhi 1759 days agowww.pango.network - All the rules to classify a Lineage ! https://www.pango.network/the-pango-nomenclature-system/statement-of-nomenclature-rules/DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies
By Shruti Paniwala 2470 days agogithub.com - DeCoSTAR computes adjacency evolutionary scenarios using a scoring scheme based on a weighted sum of adjacency gains and breakages. Solutions, both optimal and near-optimal, are sampled according to the Boltzmann–Gibbs distribution centered...mixtureS: a novel tool for bacterial strain reconstruction from reads
By BioStar 2239 days agowww.cs.ucf.edu - mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 243 simulated datasets and 195 experimental datasets, mixtureS...SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files
By Rahul Nayak 1682 days agotelatin.github.io - A general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and...Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
By Shruti Paniwala 2905 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...Kevler: Reference-free variant discovery in large eukaryotic genomes
By Jit 2445 days agogithub.com - Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs),...truvari: Structural variant comparison tool for VCFs
By Jit 2290 days agogithub.com - Structural variant comparison tool for VCFs Given benchmark and comparsion sets of SVs, calculate the recall, precision, and f-measure. Spiral Genetics Motivation2.4 Mb Genome Size for World's Biggest Virus
By Jitendra Narayan 4809 days agoA giant Pandoraviruses from alltogether different origin
