URMAP, an ultra-fast read mapper
...2×150 reads, URMAP achieves high accuracy (precision 0.998, sensitivity 0.982 and F-measure 0.990) with the strelka2 caller. However, GIAB reference variants are shown to be bias...1335 days ago
Liftoff: An accurate GFF3/GTF lift over pipeline
...-over tools which require a pre-generated “chain” file as input, Liftoff is a standalone tool that takes two genome assemblies and a reference annotation as input and outpu...1284 days ago
CoverM: Read coverage calculator for metagenomics
...dividual contigs coverm contig (help). Calculating coverage by read mapping, its input can either be BAM files sorted by reference, or raw reads and reference genomes in various formats.1153 days ago
LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data
...ssembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly...1099 days ago
1014 days ago
RNA-seq workflow: gene-level exploratory analysis and differential expression
...RNA-seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were quantified to the reference transcripts, and prepare gene...991 days ago
Understanding pango networks !
...ork/the-pango-nomenclature-system/statement-of-nomenclature-rules/ https://www.pango.network/how-does-the-system-work/what-are-pango-lineages/ Reference paper https://www.nature.com...984 days ago
ncbi-datasets-cli -- Quickstart: command line tools !
Install and use the NCBI Datasets command line tools The NCBI Datasets datasets command line tools are datasets and dataformat . Use datasets&...932 days ago
GEnView: A phylogeny based comparative genomics software to analyze the genetic environment of genes
...ed comparative genomics software to analyze the genetic environment of genes. The user can select one or several taxa and provide one or several reference protein(s). Genomes and plasm...911 days ago
889 days ago