85 Open source projects that are alternatives of or similar to readfq

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Efficient handling of FASTQ files from Python

My bioinfo toolbox

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

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

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

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

Tools for working with genomic and high throughput sequencing data.

Command line utility for manipulating Illumina-generated FastQ files.

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

UGENE is free open-source cross-platform bioinformatics software

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

Rare variant test software for next generation sequencing data

A DNA Sequence Alignment/Map (SAM) library for Clojure

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

A collection of Galaxy-related training material

💾 📃 "Reads to report" for public health and clinical microbiology

R package for analyzing single-cell RNA-seq data

A handy variant calling pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

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

Sequana: a set of Snakemake NGS pipelines

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

ABRA2

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

Collection of scripts for bacterial genomics

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

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

A library for manipulating bioinformatics sequencing formats in Apache Spark

A scalable bacterial genome assembly, annotation and analysis pipeline

Estimation of per-individual inbreeding coefficients under a probabilistic framework

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

Multi-sample somatic variant caller

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

List of IARC bioinformatics nextflow pipelines

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

Ultrafast sequence typing and gene detection from NGS raw reads

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

Faster BWA-MEM2 using learned-index

RNA-seq workflow using STAR and DESeq2

No description or website provided.

NGLess: NGS with less work

Frequently used commands in bioinformatics

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

Simple FASTQ quality assessment using Python

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

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

Utilities for analyzing next generation sequencing data.

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

An automated RNA-seq pipeline using Nextflow

Official code repository for GATK versions 4 and up

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

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

Transposon Insertion Finder - Detection of new insertions in NGS data

🐳 Bio-dockers: dockerized bioinformatic tools

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

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

Reference-based transcript discovery from long RNA read

Bioinformatics library in Kotlin

Whole Exome/Whole Genome Sequencing alignment pipeline

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