737 Open source projects that are alternatives of or similar to MTBseq_source

Data intensive science for everyone.

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

Multi-sample somatic variant caller

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

UGENE is free open-source cross-platform bioinformatics software

NGLess: NGS with less work

Official code repository for GATK versions 4 and up

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.

A simplified pipeline for ctDNA sequencing data analysis

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches

Spark VCF data source implementation for Dataframes

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦

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

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

Java utilities for Bioinformatics

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Tools to process and analyze deep sequencing data.

🔬 BEDOPS: high-performance genomic feature operations

xHLA: Fast and accurate HLA typing from short read sequence data

Rare variant test software for next generation sequencing data

An automated RNA-seq pipeline using Nextflow

simple viewer for variant call format using htslib

A Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.

A library for manipulating bioinformatics sequencing formats in Apache Spark

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

Numerical Encoding for Human Genetic Variants

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

A Java API for high-throughput sequencing data (HTS) formats.

Genome Annotation Without Nightmares

Collection of scripts for bacterial genomics

List of IARC bioinformatics nextflow pipelines

(WIP) best-practices workflow for rare disease

A package for designing compact and comprehensive capture probe sets.

Analysis pipelines for sequencing data

Ultrafast sequence typing and gene detection from NGS raw reads

🐳 Bio-dockers: dockerized bioinformatic tools

Interactive assembly and analysis of RAD-seq data sets

pythonic wrapper for htslib

Genomics using open source tools, running on GCP or AWS

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..

A simple tool to calculate reads number and total base count in FASTQ file

An interactive web portal for exploring immuno-oncology data

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

RNA-seq analysis pipeline for detection gene-fusions

Fun functional programming with pipelinable functions

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

Pytorch Implementation of GoEmotions 😍😢😱

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

Simple pure Python SAM parser and objects for working with SAM records

Swarm CI - Docker Swarm-based CI system or enhancement to existing systems.

Precision HLA typing from next-generation sequencing data

VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies

Reference-based transcript discovery from long RNA read

Toolkit for preparing genomes for submission to NCBI

Helper for dealing with secrets in kubernetes.

🚀 Automate versioning, changelog creation, README updates and GitHub releases using GitHub Actions,npm, docker or bash.

PERF is an Exhaustive Repeat Finder