SPAdes Genome Assembler

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Java utilities for Bioinformatics

A curated list of resources for learning bioinformatics.

Rapid large-scale prokaryote pan genome analysis

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

Finds SNP sites from a multi-FASTA alignment file

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

A tool to circularize genome assemblies

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Antimicrobial Resistance Identification By Assembly

MrBiomics: Composable modules and recipes automate bioinformatics for multi-omics analyses

NGLess: NGS with less work

Rare variant test software for next generation sequencing data

An efficient FASTQ manipulation suite

Get assembly statistics from FASTA and FASTQ files

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

Microsatellite Instability (MSI) detection using high-throughput sequencing data.

DeepMicrobes: taxonomic classification for metagenomics with deep learning

VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

Command line utility for manipulating Illumina-generated FASTQ files.

Infectious Disease Sequencing Platform

NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime. This allows analysing large scale datasets even with increased SNP rates or higher error rates (e.g. caused by specialized experimental protocols) and avoids biases caused by highly variable regions in the genome.

Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)

Scripts, utilities and programs for genomic bioinformatics.

No description provided.

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)

Python3 scripts to manipulate FASTA and FASTQ files