Simple ChIP-seq simulation data generator.

NGS analysis pipeline for ATAC-seq experiments.

DEmultiplexing MOnitoring Report Tool. DEMORT evaluates demultiplexed fastq files by computing various metrics.

Code and scripts used for Worth et al. 2022: "Receptor editing constrains development of phosphatidyl choline-specific B cells in VH12-transgenic mice".

conserved sequenc-based degenerate primer design tool

software for processing tuberculosis whole genome data. interface to the BWA, VarScan, SamTools etc.

NanoString classifier based on NGS training set

RAD-seq protocols for the Agilent NGS workstation option B.

Workflow to perform a Variant Calling Analysis

Extract unmapped read fragments from a sequence alignment map by evaluating it's concise idiosyncratic gapped alignment reports (CIGARs)

Mycobacterium tuberculosis classification pipeline

Ancient Environmental DNA taxonomy assignment workflow module

Neat AWS config, workflow, pipline

A pipeline for preprocessing and annotation of NGS immunoglobulin repertoire data.

Udo Stenzel's perl-ngs — a collection of Perl tools for next-generation sequencing [MIRROR]

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

Thomas' blog

A repo that contains miscellaneous Python/C++ modules/programs, a standalone Python module 'palos' by the yfish group (can be installed by pip).

Various scripts for working with NGS data in file formats such as VCF, BAM/SAM, and JSON