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The Top 23 Bioinformatics Fastq Open Source Projects

Open source projects categorized as Bioinformatics Fastq
Categories > Data Processing > Bioinformatics
Categories > Fastq
Oneliners ⭐ 1,705
Useful bash one-liners for bioinformatics.
most recent commit 9 months ago
Fastp ⭐ 1,602
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging.
total releases 1most recent commit 6 months ago
Seqtk ⭐ 1,148
Toolkit for processing sequences in FASTA/Q formats
total releases 1most recent commit a year ago
Seqkit ⭐ 1,133
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
total releases 122most recent commit 3 months ago
Bwa Mem2 ⭐ 645
The next version of bwa-mem
most recent commit 4 months ago
Vsearch ⭐ 605
Versatile open-source tool for microbiome analysis
total releases 1most recent commit 3 months ago
Seqan3 ⭐ 373
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
most recent commit 3 months ago
Juicer ⭐ 313
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
most recent commit a year ago
Bioinformatics One Liners ⭐ 277
Bioinformatics one liners from Ming Tang
most recent commit 4 years ago
Parallel Fastq Dump ⭐ 224
parallel fastq-dump wrapper
dependent packages 1total releases 9most recent commit a year agopypi parallel-fastq-dump} Downloads
Pyfastx ⭐ 211
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
dependent packages 20total releases 68most recent commit 5 months agopypi pyfastx} Downloads
Afterqc ⭐ 157
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
most recent commit 6 years ago
Rasusa ⭐ 156
Randomly subsample sequencing reads to a specified coverage
total releases 11most recent commit 4 months ago
Genomics ⭐ 154
A collection of scripts and notes related to genomics and bioinformatics
most recent commit 2 years ago
Ngless ⭐ 141
NGLess: NGS with less work
total releases 5most recent commit a year ago
Biofast ⭐ 132
Benchmarking programming languages/implementations for common tasks in Bioinformatics
most recent commit 3 years ago
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.
most recent commit 5 months ago
Mutscan ⭐ 127
Detect and visualize target mutations by scanning FastQ files directly
most recent commit 2 years ago
Fastqt ⭐ 109
FastQC port to Qt5: A quality control tool for high throughput sequence data.
most recent commit 4 years ago
Fqtools ⭐ 105
An efficient FASTQ manipulation suite
most recent commit 4 years ago
Readfq ⭐ 105
Fast multi-line FASTA/Q reader in several programming languages
most recent commit 5 years ago
Isoquant ⭐ 98
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
most recent commit 3 months ago
Seqfu2 ⭐ 96
🚀 seqfu - Sequece Fastx Utilities
most recent commit 4 months ago
The 6 Most Depended On Bioinformatics Fastq Open Source Projects
Pyfastx ⭐ 211
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
dependent packages 20total releases 68latest release November 25, 2023most recent commit 5 months agopypi pyfastx} Downloads
Dnaio ⭐ 52
Efficiently read and write sequencing data from Python
dependent packages 15total releases 23latest release November 20, 2023most recent commit 3 months agopypi dnaio} Downloads
Fastaq ⭐ 45
Python3 scripts to manipulate FASTA and FASTQ files
dependent packages 7total releases 21latest release February 19, 2018most recent commit 2 years agopypi pyfastaq} Downloads
Fuc ⭐ 38
Frequently used commands in bioinformatics
dependent packages 2total releases 44latest release September 09, 2023most recent commit 7 months agopypi fuc} Downloads
Fasta ⭐ 5
This package enables you to deal with biological sequence files easily.
dependent packages 1total releases 20latest release January 18, 2023most recent commit 7 months agopypi fasta} Downloads
Parallel Fastq Dump ⭐ 224
parallel fastq-dump wrapper
dependent packages 1total releases 9latest release April 23, 2019most recent commit a year agopypi parallel-fastq-dump} Downloads
The 10 Latest Releases In Bioinformatics Fastq Open Source Projects
Pyfastx ⭐ 211
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
dependent packages 20total releases 68latest release November 25, 2023most recent commit 5 months agopypi pyfastx} Downloads
Dnaio ⭐ 52
Efficiently read and write sequencing data from Python
dependent packages 15total releases 23latest release November 20, 2023most recent commit 3 months agopypi dnaio} Downloads
Seqkit ⭐ 1,133
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
total releases 122latest release November 18, 2023most recent commit 3 months ago
Celescope ⭐ 73
Single Cell Analysis Pipelines
total releases 59latest release November 16, 2023most recent commit 3 months ago
Fasten ⭐ 57
:construction_worker: Fasten toolkit, for streaming operations on fastq files
total releases 8latest release October 28, 2023most recent commit 5 months ago
Fuc ⭐ 38
Frequently used commands in bioinformatics
dependent packages 2total releases 44latest release September 09, 2023most recent commit 7 months agopypi fuc} Downloads
Rasusa ⭐ 156
Randomly subsample sequencing reads to a specified coverage
total releases 11latest release April 06, 2023most recent commit 4 months ago
Fqgrep ⭐ 75
Grep for FASTQ files
total releases 2latest release January 25, 2023most recent commit 10 months ago
Fasta ⭐ 5
This package enables you to deal with biological sequence files easily.
dependent packages 1total releases 20latest release January 18, 2023most recent commit 7 months agopypi fasta} Downloads
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