Polymorphic Edge Detection - An efficient polymorphism detector for NGS data

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

Snakemake pipeline for Popoolation and Popoolation2

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

Automated mitochondrial genome assembly using SRA public data

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…

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.

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

Allele-specific alignment sorting

The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline

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

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

A software to detect virome-wide integrations

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

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

Collection of scripts for bacterial genomics

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

2019 Genomics Epidemiology Workshop at Academia Sinica

Integrative Pipeline for Splicing Analyses (IPSA) in Nextflow

A tool for tRNA-derived small RNA annotation