Collection of scripts for bacterial genomics

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

Allele-specific alignment sorting

Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay

The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline

Process m6A/MeRIP-seq data in a single or batch job mode

A software to detect virome-wide integrations

Integrative Pipeline for Splicing Analyses (IPSA) in Nextflow

A tool for tRNA-derived small RNA annotation

Transposon Insertion Finder - Detection of new TE insertions in NGS data

2019 Genomics Epidemiology Workshop at Academia Sinica

Snakemake pipeline for Popoolation and Popoolation2

Polymorphic Edge Detection - An efficient polymorphism detector for NGS data

Hi-C data processing pipeline (with Dragen, HiSAT2, or STAR aligner)

Sanyojan is a highly sensitive, hybrid genome assembler.

🔍 💊 Detection of low-frequency SNPs in next-generation sequencing data of Mycobacterium tuberculosis complex strains

Computational Suite For Bioinformaticians and Biologists (CSBB) provides 18 modules focused on analytical tasks like performing upper-quantile normalization, interactive visualization and next generation sequencing pipelines. CSBB now also has capability to process public data. Providing User with End to End pipeline experience

Resequencing project for Fusarium graminearum

Grouped Read Testing

A script to report depth of coverage from BAM/SAM/CRAM file or parse the output generated from "samtools depth"