Find hypermutations or other patterns in nucleotide sequences

Light-weight, browser-based ROLAP pivot tables on top of DuckDB-WASM

Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data

✂️ ⚡ Rapid haploid variant calling and core genome alignment

SRA Tools

Sequences from HIV Easily Reconstructed

de novo virus assembler of Illumina paired reads

lightweight C implementation of name collating BAM file input and BAM file output

SMALT sequence aligner

ARCHIVED: see viral-ngs repo

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

Sequences from HIV Easily Reconstructed

Cntlm is an NTLM / NTLM Session Response / NTLMv2 authenticating HTTP proxy intended to help you break free from the chains of Microsoft proprietary world. More info on http://cntlm.sourceforge.net…

R implementation of hypermut 2.0 algorithm

A comprehensive pipeline for HIV drug resistance identification, variant evaluation, and surveillance.

TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomic NGS data. This flexible tool was developed with various us…

This repository contains scripts and data for training and utilizing machine learning classifiers to predict qPCR cross-amplification.

A sample sheet generator for Illumina sequencing

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

Module for reading ABI Sanger sequencing trace files

snipit: summarise snps relative to your reference sequence

🧬 Chromatogram File Utils, a package that integrates trace visualization, mutation calling and quality control for Sanger sequencing data.

ABIF parser, writer and generator