Unix, R and python tools for genomics and data science

the pangenome graph builder

Download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.

MUM&Co uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation

This repository provides source code for several pipelines dedicated to the alignment of nucleotide coding sequences that are based on MACSE. These pipelines are mostly bash scripts encapsulated wi…

Convert RepeatMasker ".out" file into a gff3 with colors!!!

methods for orphan gene prediction paper optimization

PG-SCUnK mesure quality of Pan-Genome Graphs using Single Copy and Universal k-mers

Whole-genome bioinformatic pipeline for pooled or individual-based NGS data using bash and R

Generate alternative long reads with the help of target`s assemblies, target`s PacBio HiFi reads and reference genome.

SRY: an effective method for sorting long-read of sex-limited (Y or W) chromosome.

Genome Assembly 102

Analyses of sex chromosome evolution in songbirds

genotype and visualize structural variants in the human pangenome graphs

Workflow to visualize pggb graphs in jbrowse

A simple visualisation tool for Multiple Sequence Alignment.

EvANI: genomic distance evaluation pipeline and benchmarking dataset

hard mode all genomes alignment

Scripts for manually classifying reads and make figures

A comparative annotation toolkit (CAT) pipeline for 301 Drosophila genomes.

SRY: an effective method for sorting long-read of sex-limited (Y or W) chromosome. (Developed by WANG Xiaobo from CAAS)