85 Open source projects that are alternatives of or similar to fastq-and-furious

My bioinfo toolbox

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

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

A method for circular DNA detection based on probabilistic mapping of ultrashort reads

A collection of Galaxy-related training material

R package for analyzing single-cell RNA-seq data

Sequana: a set of Snakemake NGS pipelines

A method for variant graph genotyping based on exact alignment of k-mers

Simple FASTQ quality assessment using Python

ABRA2

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

Sync paired-end FASTA/Q files and keep singleton reads

Tools for working with genomic and high throughput sequencing data.

myVCF: a web-based platform for target and exome mutations data management

UGENE is free open-source cross-platform bioinformatics software

Collection of scripts for bacterial genomics

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

Command line utility for manipulating Illumina-generated FastQ files.

Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical biologists and wet-lab personnel to do metagenomics/viromics analyses themselves, without bioinformatics expertise.

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

Estimation of per-individual inbreeding coefficients under a probabilistic framework

(No maintenance) Detect gene fusion directly from raw fastq files

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

A workflow for creating small NGS test data sets, useful for continuous integration.

Estimation of pairwise distances under a probabilistic framework

Customizable workflows based on snakemake and python for the analysis of NGS data

No description or website provided.

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

🐳 Bio-dockers: dockerized bioinformatic tools

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

C library for high-throughput sequencing data formats

RNA-seq workflow using STAR and DESeq2

Faster BWA-MEM2 using learned-index

NGLess: NGS with less work

An automated RNA-seq pipeline using Nextflow

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

A library for manipulating bioinformatics sequencing formats in Apache Spark

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

RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.

A scalable bacterial genome assembly, annotation and analysis pipeline

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

Java utilities for Bioinformatics

Official code repository for GATK versions 4 and up

A course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Multi-sample somatic variant caller

Transposon Insertion Finder - Detection of new insertions in NGS data

An easy-to-use way for running Galaxy workflows.

A robust model for quantitative comparison of ChIP-Seq data sets.

Utilities for analyzing next generation sequencing data.

Data intensive science for everyone.

Rare variant test software for next generation sequencing data

Tools to process and analyze deep sequencing data.

Ultrafast sequence typing and gene detection from NGS raw reads

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

Whole Exome/Whole Genome Sequencing alignment pipeline

Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework

Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay