Top 20 next-generation-sequencing open source projects

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

DNAscan is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring very little computational effort and memory usage.

Assembling the cause of phenotypes and genotypes from NGS data

My own tools code for NGS data analysis (Next Generation Sequencing)

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

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

Command line utility for manipulating Illumina-generated FastQ files.

Utilities for analyzing next generation sequencing data.

Multilocus sequence typing by blast using the schemes from PubMLST

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

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

Improve the quality of a denovo assembly by scaffolding and gap filling

Minor Variant Calling and Phasing Tools

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

Project Manager for NGS data analysis

Finds SNP sites from a multi-FASTA alignment file

Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer

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

Rare variant test software for next generation sequencing data