Supernova: generates phased, whole-genome de novo assemblies from a Chromium-prepared library.
Supernova generates phased, whole-genome de novo assemblies from a Chromium-...va should be run using 38-56x coverage of the genome.• Somewhat higher covera...ease note that we have not extensively tested genomes larger than human, and any g...1499 days ago
1480 days ago
PhiSpy: PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes
PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes. Given an annotated genome it will use several approaches to id...1468 days ago
Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies
Liftoff, an accurate tool that maps annotations in...input, Liftoff is a standalone tool that takes two genome assemblies and a reference an...on as input and outputs an annotation of the target genome.1468 days ago
SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator
SVEngine (Structural Variants Engine) SVEngine is a multi-purpose and self-contained simulator for whole genome scale spike-in of thousands of SV events of various types in both singl...1465 days ago
merqury: Evaluate genome assemblies with k-mers
Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating a...1465 days ago
ShadowCaster: a hybrid approach for the detection of horizontal gene transfer events in prokaryotes
ShadowCaster implements an evolutionary model to calculate Bayesian likelihoods for...;alien genes’ with an unusual sequence composition according to the host genome background to detect HGT even...1455 days ago
wgd—simple command line tools for the analysis of ancient whole-genome duplications
wgd is a easy to use command-line tool for KS distribution construction named wgd. The wgd suite provides commonly used KS and colinearity analysis...1446 days ago
1446 days ago
proActiv: Estimation of Promoter Activity from RNA-Seq data
proActiv is an R package that estimates promoter activity from RNA-Seq data. proActiv uses aligned reads and genome annotations as input, and pro...1425 days ago