Allele-specific alignment sorting

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

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.

The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline

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

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

A software to detect virome-wide integrations

DecontaMiner is a tool designed and developed to investigate the presence of contaminating sequences in unmapped NGS data. It can suggest the presence of contaminating organisms in sequenced samples, that might derive either from laboratory contamination or from their biological source, and in both cases can be considered as worthy of further in…

Integrative Pipeline for Splicing Analyses (IPSA) in Nextflow

2019 Genomics Epidemiology Workshop at Academia Sinica

Automated pipeline for HGT and contaminant detection in an assembled, annotated genome

Snakemake pipeline for Popoolation and Popoolation2

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

A tool for tRNA-derived small RNA annotation

Resequencing project for Fusarium graminearum

Polymorphic Edge Detection - An efficient polymorphism detector for NGS data

dePoP - determination of polymorphism carriers from overlapping DNA pools

Sanyojan is a highly sensitive, hybrid genome assembler.

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