Miropeats: discovers regions of sequence similarity amongst any set of DNA sequences
Miropeats discovers regions of sequence similarity amongst any set of DNA sequences and then presents this similarity information graphically. Sequence similarity searching...1772 days ago
1767 days ago
chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes
chromoMap provides interactive, configurable and elegant graphics visualization of chromosomes or chromosomal regions allowing users to map chromosome elements (like ge...1760 days ago
mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as would be us...1689 days ago
1613 days ago
CLARK: Fast, accurate and versatile sequence classification system
CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article fo...1599 days ago
chromosight: Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps
Python package to detect chromatin loops (and other patterns) in Hi-C contact maps. Stable version with pip: pip3 install --user chromosight Stable version with conda...1562 days ago
CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes
The pipeline can use information from scaffolded assemblies (for example from HiC or 10X Genomics), or even from diverged (~65-100 Mya) reference genomes for ordering the co...1210 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...1459 days ago
pggb: the pangenome graph builder
This pangenome graph construction pipeline renders a collection of sequences into a pangenome graph (in the variation graph model). Its goal is to build a graph that is loca...1388 days ago