Awesome Open Source

Programming Languages

Search results for fastq

493 search results found

Oneliners ⭐ 1,705

Useful bash one-liners for bioinformatics.

Fastp ⭐ 1,602

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

Seqtk ⭐ 1,148

Toolkit for processing sequences in FASTA/Q formats

Seqkit ⭐ 1,133

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

Fast, in memory work queue

Bwa Mem2 ⭐ 645

The next version of bwa-mem

Vsearch ⭐ 605

Versatile open-source tool for microbiome analysis

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

Trimgalore ⭐ 382

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Bactopia ⭐ 281

A flexible pipeline for complete analysis of bacterial genomes

Bioinformatics One Liners ⭐ 277

Bioinformatics one liners from Ming Tang

Basecalling Comparison ⭐ 273

A comparison of different Oxford Nanopore basecallers

Krakentools ⭐ 242

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

Parallel Fastq Dump ⭐ 224

parallel fastq-dump wrapper

Pyfastx ⭐ 211

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

Fastq Dl ⭐ 174

Download FASTQ files from SRA or ENA repositories.

Windowed Adaptive Trimming for fastq files using quality

Afterqc ⭐ 157

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

Randomly subsample sequencing reads to a specified coverage

A high performance and compression ratio compressor for genomic data, powered by GTXLab of Genetalks.

Genomics ⭐ 154

A collection of scripts and notes related to genomics and bioinformatics

Rust Bio Tools ⭐ 154

A set of command line utilities based on Rust-Bio.

FASTQ sequence quality visualisation with Emoji

Genozip ⭐ 144

A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too

Rmats Turbo ⭐ 144

Nanopack ⭐ 143

Easily install all nanopack scripts together

NGLess: NGS with less work

Efficient clustering of next generation sequences

Biofast ⭐ 132

Benchmarking programming languages/implementations for common tasks in Bioinformatics

Seq2science ⭐ 132

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

Viral Ngs ⭐ 129

Viral genomics analysis pipelines

Mutscan ⭐ 127

Detect and visualize target mutations by scanning FastQ files directly

Ngs Bits ⭐ 121

Short-read sequencing tools

Qiita - A multi-omics databasing effort

Fastq Pair ⭐ 115

Match up paired end fastq files quickly and efficiently.

A fast lossless FASTQ compressor with ultra-high compression ratio

FastQC port to Qt5: A quality control tool for high throughput sequence data.

Fastx_toolkit ⭐ 109

FASTA/FASTQ pre-processing programs

Ngscheckmate ⭐ 106

Software program for checking sample matching for NGS data

Fast multi-line FASTA/Q reader in several programming languages

Fqtools ⭐ 105

An efficient FASTQ manipulation suite

Isoquant ⭐ 98

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

🚀 seqfu - Sequece Fastx Utilities

Simple FASTQ quality assessment using Python

Fetchngs ⭐ 93

Pipeline to fetch metadata and raw FastQ files from public and private databases

Assembly Stats ⭐ 92

Get assembly statistics from FASTA and FASTQ files

Pandaseq ⭐ 91

PAired-eND Assembler for DNA sequences

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

Adapterremoval ⭐ 87

AdapterRemoval v2 - rapid adapter trimming, identification, and read merging

Pipeline Structural Variation ⭐ 87

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

Fastq Tools ⭐ 86

Small utilities for working with fastq sequence files.

Genefuse ⭐ 86

Gene fusion detection and visualization

Soapnuke ⭐ 85

A Tool for integrated Quality Control and Preprocessing on FASTQ or BAM/CRAM files

Mcclintock ⭐ 83

Meta-pipeline to identify transposable element insertions using next generation sequencing data

Illumina Utils ⭐ 82

A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).

Nullarbor ⭐ 80

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

Ngsutils ⭐ 80

Tools for next-generation sequencing analysis

Ratatosk ⭐ 76

Hybrid error correction of long reads using colored de Bruijn graphs

Grep for FASTQ files

Celescope ⭐ 73

Single Cell Analysis Pipelines

Neat Genreads ⭐ 72

NEAT read simulation tools

Phylosift ⭐ 68

Phylogenetic and taxonomic analysis for genomes and metagenomes

qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.

Scatac Pro ⭐ 64

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data

Nanostat ⭐ 63

Create statistic summary of an Oxford Nanopore read dataset

Opengene.jl ⭐ 61

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

FASTA and FASTQ parsing in Rust

COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)

fastqcr: Quality Control of Sequencing Data

👷 Fasten toolkit, for streaming operations on fastq files

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.

Pyflow Chipseq ⭐ 55

a snakemake pipeline to process ChIP-seq files from GEO or in-house

Command line utility for manipulating Illumina-generated FASTQ files.

Efficiently read and write sequencing data from Python

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

Model and predict short DNA sequence features with neural networks

Poreplex ⭐ 51

A versatile sequenced read processor for nanopore direct RNA sequencing

A C++ drop-in replacement of FastQC to assess the quality of sequence read data

Fastq And Furious ⭐ 49

Efficient handling of FASTQ files from Python

Metacache ⭐ 49

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

Fastx.jl ⭐ 48

Parse and process FASTA and FASTQ formatted files of biological sequences.

A genomics-proteomics toolkit

A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.

Bamtofastq ⭐ 45

Convert 10x BAM files to the original FASTQs compatible with 10x pipelines

Python3 scripts to manipulate FASTA and FASTQ files

Umicollapse ⭐ 44

Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.

Bam Tricks ⭐ 44

Tip and tricks for BAM files

W2rap Contigger ⭐ 44

An Illumina PE genome contig assembler, can handle large (17Gbp) complex (hexaploid) genomes.

Pauvre: QC and genome browser plotting Oxford Nanopore and PacBio long reads.

Cfdnapattern ⭐ 42

Pattern Recognition for Cell-free DNA

Fastq Screen ⭐ 42

Detecting contamination in NGS data and multi-species analysis

Bioinformatic infrastructure libraries

Ngspeciesid ⭐ 41

Reference-free clustering and consensus forming of long-read amplicon sequencing

PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores

MutMap pipeline to identify causative mutations responsible for a phenotype

Related Searches

Python Fastq (438)

Fasta Fastq (230)

Pipeline Fastq (218)

Genome Fastq (182)

Sequencing Fastq (149)

Bioinformatics Fastq (134)

Shell Fastq (125)

C Plus Plus Fastq (115)

Perl Fastq (101)

1-100 of 493 search results

Privacy | About | Terms | Follow Us On Twitter

Copyright 2018-2024 Awesome Open Source. All rights reserved.