SLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.
This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds. Here is an illustration of this pipeline:1540 days ago
LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
...thods or only used for filtering. https://github.com/CSB5/lofreq http://csb5.github.io/lofreq/installation/ https://github.com/CSB5/lofreq/tree/master/dist1537 days ago
Nextflow: Data-driven computational pipelines
Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting la...1535 days ago
U-Plot: Genome U-Plot sample implementation
The Genome U-Plot is a JavaScript tool to visualize Chromosomal abnormalities in the Human Genome using a U-shape layout.1523 days ago
chromosight: Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps
...rge chromosight or, if you want to get the latest development version: pip3 install --user -e git+https://github.com/koszullab/chromosight.git@master#egg=chromosight1503 days ago
flexidot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses
FlexiDot is a cross-platform dotplot suite generating high quality self, pairwise and all-against-all visualizations. To improve dotplot suitability for comparison of c...1471 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 t...1151 days ago
1373 days ago
SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis
SHAMAN is a shiny application for differential analysis of metagenomic data (16S, 18S, 23S, 28S, ITS and WGS) including bioinformatics treatment of raw reads for target...1356 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...1328 days ago