1770 days ago
1736 days ago
ALF--a simulation framework for genome evolution.
Artificial Life Framework (ALF) simulates a root genome into a number of related genomes. Result files include the resulting gene sequences, true...net, Christophe Dessimoz: ALF - A Simulation Framework for Genome Evolution. Mol Biol Evol...1717 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
...accurate reference-guided scaffolding of draft genomes. bioRxiv 2019. RaGOO is a tool for coalescing genome assembly contigs into pseudoc...construction takes less than a minute and the whole pipeline with SV calling takes...1713 days ago
mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
mosdepth can output: per-base depth about 2x as fast sam...tools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a...or above a given threshold for each chromosome and genome-wide.quantized output that me...1692 days ago
simuG: a general-purpose genome simulator
Simulated genomes with pre-defined and random genomic variants can be very useful for benchma...n). The simplicity and versatility of simuG make it a unique general-purpose genome simulator for a wide-range of...1681 days ago
RepeatModeler2: automated genomic discovery of transposable element families
RepeatModeler2 represents a valuable addition to the genome annotation toolkit that will enhance the identification and study of TEs in eukaryotic genome sequences. RepeatModeler2 is...1677 days ago
HaploTypo: a variant-calling pipeline for phased genomes
An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, most...h heterozygous variant called on a phased reference genome. Availability and Implementa...1660 days ago
1656 days ago
ClinCNV: Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
ClinCNV detects CNVs in germline and somatic context in NGS data (targeted and whole-genome). We work in cohorts, so it makes sense to try ClinCNV if you have more than 10 samp...1631 days ago