1952 days ago
1943 days ago
TRITEX sequence assembly pipeline for Triticeae genomes
The pipeline is open-source and hosted in a public Bitbucket repository....work on heterozygous or autopolyploid genomes. A protocol for generating chromosome-conformation capture sequenci...1730 days ago
1719 days ago
chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes
chromoMap provides interacti...ant graphics visualization of chromosomes or chromosomal regions allowing users to map chromosome elements (like genes,SNPs etc...fic range determined based on chromosome length) that, on hover, shows...as distinct colors. creating chromosome heatmaps. adjusting chromoso...1712 days ago
mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
mosdepth can output: per-base depth about 2x as fast...ses covered at or above a given threshold for each chromosome and genome-wide.quantized out...the given thresholds.A summary of mean depths per chromosome and within specified regions...1642 days ago
1565 days ago
CLARK: Fast, accurate and versatile sequence classification system
CLARK, a method based on a supervised sequence classification using discriminative...nown bacterial genomes, and (2) the assignment of BAC clones and transcript to chromosome arms/centromeres (in the abse...1552 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 co...1515 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...o current state of the art methods. For smaller vertebrate genomes (~1 Gbp) chromosome scale assemblies can be achie...1163 days ago