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An open API service indexing awesome lists of open source software.

Projects in Awesome Lists tagged with fasta

A curated list of projects in awesome lists tagged with fasta .

https://github.com/shenwei356/seqkit

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

bioinformatics cross-platform fasta fastq golang manipulation sequence tool toolkit

Last synced: 29 Dec 2025

https://github.com/jupyterlab/jupyter-renderers

Renderers and renderer extensions for JupyterLab

fasta geojson jupyterlab jupyterlab-extension katex plotly vega vega-lite

Last synced: 14 May 2025

https://github.com/mdshw5/pyfaidx

Efficient pythonic random access to fasta subsequences

bgzf bioinformatics dna fasta genomics indexing protein python samtools

Last synced: 14 May 2025

https://github.com/seqan/seqan3

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

bioinformatics blast cpp-concepts cpp20 fasta fastq fm-index modern samtools seqan sequence-alignment sequence-analysis

Last synced: 01 Mar 2026

https://github.com/samtools/htsjdk

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

bam cram dna fasta genomics java java-api ngs sam sequencing vcf

Last synced: 14 May 2025

https://github.com/lmdu/pyfastx

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

assembly bioinformatics biology dna fasta fastq genome python sequence

Last synced: 15 May 2025

https://github.com/mbhall88/rasusa

Randomly subsample sequencing reads or alignments

alignment bam bioinformatics coverage downsample fasta fastq genome-analysis random rust subsampling

Last synced: 19 Feb 2026

https://github.com/edgardomortiz/vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

alignment binary convert-snps diploid fasta haploid nexus outgroup phylip phylip-matrix phylogenetic-analysis phylogenetics polyploid snapp snps vcf vcf-files vcf-format

Last synced: 28 Feb 2026

https://github.com/igordot/genomics

A collection of scripts and notes related to genomics and bioinformatics

bioinformatics dna fast5 fasta fastq genomics gtf illumina nanopore science sequencing vcf workflow

Last synced: 21 Jan 2026

https://github.com/pydna-group/pydna

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.

anaconda assembly-strategies bioinformatics biology biopython cloning-strategies dna fasta gel gel-electrophoresis gel-simulation genbank gibson-assembly jupyter jupyter-notebook jupyter-notebooks pydna python simulation

Last synced: 06 Feb 2026

https://github.com/divonlan/genozip

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

23andme bam bgzip bwa compression cram fasta fastq genomics gvf gzip sam samtools vcf

Last synced: 13 May 2026

https://github.com/eead-csic-compbio/get_homologues

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

annotation bacteria clustering fasta genbank pangene pangenome plants transcriptome

Last synced: 11 Feb 2026

https://github.com/telatin/seqfu2

:rocket: seqfu - Sequece Fastx Utilities

bioconda bioinformatics bioinformatics-tool fasta fastq genomics ngs sequencing

Last synced: 21 Oct 2025

https://github.com/smaegol/plasflow

Software for prediction of plasmid sequences in metagenomic assemblies

classification contigs fasta metagenome metagenome-assembly metagenomes plasflow plasmid plasmid-sequences plasmids prediction tensorflow

Last synced: 21 Jul 2025

https://github.com/chrovis/cljam

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

2bit bam bcf bed bigwig bioinformatics clojure cram fasta fastq genomics gff sam vcf wig

Last synced: 16 May 2025

https://github.com/biojulia/fastx.jl

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

bio biojulia fasta fasta-files fasta-format fastq fastq-files fastq-format file-format julia parsing

Last synced: 05 Apr 2025

https://github.com/rcs333/VAPiD

VAPiD: Viral Annotation and Identification Pipeline

annotations bioinformatics biology fasta genbank metadata ncbi ngs virology virus

Last synced: 23 Mar 2025

https://github.com/brentp/hts-python

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

bam bioinformatics fasta genomics htslib python sam

Last synced: 21 Mar 2025

https://github.com/sbslee/fuc

Frequently used commands in bioinformatics

api bam bed bioinformatics cli cram fasta fastq gff gtf maf sam vcf visualization

Last synced: 06 Apr 2025

https://github.com/opengene/uniquekmer

Generate unique KMERs for every contig in a FASTA file

bioinformatics fasta kmer ngs sequencing unique virus

Last synced: 10 Apr 2025

https://github.com/rkmlab/perf

PERF is an Exhaustive Repeat Finder

biopython fasta genome genomics microsatellites repeats sequence simple ssr tandem

Last synced: 14 Jan 2026

https://github.com/jfjlaros/demultiplex

Versatile FASTA/FASTQ demultiplexer.

demultiplex fasta fastq ngs

Last synced: 04 May 2025

https://github.com/mbhall88/psdm

Compute a pairwise SNP distance matrix from one or two alignment(s)

alignment bioinformatics distance fasta matrix pairwise rust snp

Last synced: 17 Mar 2025

https://github.com/brwnj/idplot

compare sequences to a shared root reference sequence.

fasta nextflow plotly recombination sars-cov-2 virus

Last synced: 10 Mar 2026

https://github.com/benhid/pymsa

Scoring multiple sequence alignments with Python

entropy fasta gaps msa python score sequence-alignment sumofpairs

Last synced: 19 Aug 2025

https://github.com/yhoogstrate/fastafs

toolkit for file system virtualisation of random access compressed FASTA, FAI, DICT & TWOBIT files

2bit compression dna-sequences fasta filesystem fuse-filesystem

Last synced: 17 Jan 2026

https://github.com/xthua/bacant

This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.

amr bacteria fasta integron transposon

Last synced: 14 Jan 2026

https://github.com/moold/kseq-rs

A FASTA/FASTQ format parser library

fasta fastq

Last synced: 18 Aug 2025

https://github.com/incertae-sedis/smof

Explore and analyze biological sequence data

bioinformatics biology fasta genomics sequence sequence-analysis

Last synced: 17 Dec 2025

https://github.com/kronopt/fastaparser

A Python FASTA file Parser and Writer.

fasta fasta-parser fasta-reader fasta-writer parser python python-3

Last synced: 15 Apr 2025

https://github.com/carlobaldassi/fastaio.jl

Utilities to read/write FASTA format files in Julia

bioinformatics fasta julia

Last synced: 13 Apr 2025

https://github.com/ga4gh/refget

GA4GH Refget specifications docs

collection digest fasta sequence

Last synced: 23 Jan 2026

https://github.com/qdata/gakco-svm

ECML16: GaKCo: a Fast Gapped k-mer string Kernel using Counting

fasta gakco-svm kernel

Last synced: 01 May 2025

https://github.com/pwilmart/fasta_utilities

Utilities for downloading and managing protein FASTA files.

ensembl fasta ncbi protein-databases python3 uniprot

Last synced: 28 Oct 2025

https://github.com/biomadeira/biodownloader

📦 A Command Line Tool for downloading protein structures, sequences and MSAs

bioinformatics cath cli fasta gff mmcif pdb pfam sifts

Last synced: 16 Jul 2025

https://github.com/xyaneon/xyaneon.bioinformatics.fasta

A .NET Standard library for working with FASTA genetic sequence files.

bioinformatics biology csharp dotnet fasta netstandard

Last synced: 20 Jun 2025

https://github.com/pdimens/bio-bin

Handy reusable bioinformatic scripts

bioinformatics fasta genome-analysis genomics julia

Last synced: 11 Apr 2025

https://github.com/holgerbrandl/kutils

A random collection of kotlin utilities

bioinformatics fasta fastq kotlin kotlin-utilities kscript mpi-cbg

Last synced: 10 Jul 2025

https://github.com/ctskennerton/fxtract

Extract sequences from a fastx file given a subsequence or identifier

bioinformatics fasta fastq

Last synced: 21 Mar 2025

https://github.com/haradama/plasmidpicker

Software to identify plasmid sequence data from metagenome using logistic regression and Minhash

bioinformatics classification contigs fasta logistic-regression metagenome metagenomics minhash plasmids

Last synced: 13 Apr 2025

https://github.com/dillondaudert/proteindatasets

Creating and manipulating various protein sequence-structure datasets using Python, Julia, and other tools.

bioinformatics biopython blast dataset dssp fasta julia jupyter jupyter-notebook pandas protein psiblast python3 secondary structure tensorflow uniref50

Last synced: 10 Apr 2025

https://github.com/pgarrett-scripps/fastaframes

Python package to convert between FASTA files and Pandas DataFrames.

bioinformatics fasta mass-spectrometry package pandas protein protein-sequences proteomics python

Last synced: 31 Jul 2025

https://github.com/wang-q/faops

faops operates fasta files

fasta kent-utilities klib

Last synced: 21 Jun 2025

https://github.com/eneskemalergin/z-fasta

A zero-dependency FASTA indexer and extractor written in Zig. Speeds up standard samtools workflows by ~17x using SIMD and mmap.

bioinformatics fasta proteomics ziglang

Last synced: 07 Apr 2026

https://github.com/orangeSi/biokits

bioinformatics tools

bioinformatics fasta

Last synced: 10 Jul 2025

https://github.com/not-a-feature/minifasta

An small FASTA toolbox for small to medium size projects without dependencies.

bioinformatics fasta python reader-writer toolbox

Last synced: 21 Oct 2025

https://github.com/orangesi/biokits

bioinformatics tools

bioinformatics fasta

Last synced: 12 Feb 2026

https://github.com/jeanmanguy/uniprot-fasta-header

Rust crate to parse Uniprot FASTA headers.

bioinformatics fasta parsing protein rust uniprot

Last synced: 22 Jun 2025

https://github.com/peterhil/serpent

Serpent is an exploration into DNA sequences, codons, amino acids and genome data

bioinformatics fasta sequencing

Last synced: 06 Feb 2026

https://github.com/haradama/phash

Software to identify known plasmid sequence from metagenomic assembly using Minhash

bioinformatics biology contigs fasta golang metagenome metagenomics minhash plasmid plasmids

Last synced: 05 Mar 2025

https://github.com/gagniuc/genomin

Genomin is an implementation for large-scale genomic analysis. It is made in Visual Basic 6.0 (VB6). It uses the seek method to generate buffers from large FASTA files (over 8 Gb).

bioinformatics fasta files genetics genomics genomin vb6

Last synced: 05 Mar 2026

https://github.com/vbaliga/genbank_downloadr

🔬 Batch downloading of DNA or protein sequences from GenBank

fasta genbank genes purrr r rentrez rstats tidyverse

Last synced: 03 Apr 2025

https://github.com/biocentral/bio_flutter

Working with biological data in flutter.

dart embeddings fasta flutter protein protein-protein-interaction umap

Last synced: 07 Mar 2026

https://github.com/orangesi/pykits

simple python script for bioinformatics

bioinformatics-scripts biopython fasta fire-python pandas-python python3

Last synced: 28 Feb 2025

https://github.com/raw-lab/metaome_stats

Statistical package for metaome denovo assembly results.

fasta genome metagenome metagenome-assembly metaome-stats metatranscriptomics transcriptomics

Last synced: 16 Jan 2026

https://github.com/corneliusroemer/fasta_zstd_sqlite

Efficiently store FASTA sequences in sqlite compressed with sidecar zstd dictionary

bioinformatics fasta genomic-epidemiology sqlite virus-bioinformatics zstd zstd-dictionary

Last synced: 19 May 2026

https://github.com/vaibhavvikas/fasta-sequence-retrieval

Python Project to extract the amino acid sequences using the nucleotides accession numbers retrieved from the NCBI.

fasta ncbi

Last synced: 26 Feb 2025

https://github.com/romgrk/bioinformatics-parser

Simple nodejs fasta/fastq parser

bioinformatics fasta fastq

Last synced: 14 Apr 2025

https://github.com/antonoresten/typedfastx.jl

FASTX records with typed sequences and optional qualities.

bio dna fasta fastq fastx quality sequence typed

Last synced: 10 Mar 2026

https://github.com/haschka/sequence_in_sequence_finder

A tool that finds a nucleic sub-sequence string ( from a FASTA file ) in a FASTA file using the fourier transform.

bioinformatics bioinformatics-tool fasta fasta-files fourier-transform fourier-transformation sequence sequence-finder unix-tools

Last synced: 30 May 2026

https://github.com/shuyib/from_cell_to_statistics

An introduction to Genomic Data Science/Bioinformatics.

bioinformatics biology cancer dna fasta fastq gwas molecular-biology protein rna

Last synced: 29 Jul 2025

https://github.com/abhijeetsingh1704/dupremover

Removes duplicate sequences in multifasta file

fasta fasta-format fasta-sequences unique

Last synced: 17 Aug 2025

https://github.com/mnsmar/rnadna

Convert sequence representation RNA - DNA for FASTA/Q

bioinformatics dna fasta fastq go rna

Last synced: 06 May 2025

https://github.com/rigdenlab/crops

Cropping and Renumbering Operations for PDB structure and Sequence files

bioinformatics fasta pdb

Last synced: 17 Jan 2026

https://github.com/cdcgov/clean-genes

A rust crate that automatically cleans up a gene alignment by trimming to ORF and identifying and/or removing problematic sequences.

bioinformatics cdc-influenza-division data-cleaning data-normalisation data-normalization data-science fasta ncird ncird-id sequence-alignment sequence-analysis sequence-annotation

Last synced: 01 Mar 2026

https://github.com/lucblassel/fastago

CLI to deal with fasta files written in Go

bioinformatics fasta go hacktoberfest sequences

Last synced: 26 Jan 2026

https://github.com/nylander/fastear

FastEAR - Fast(er) Extraction of Alignment Regions from FASTA

faidx fasta samtools

Last synced: 05 Mar 2025

https://github.com/pprattis/chromosome-last-random-nucleotide-game

A Python script that implements a two player strategic game with two sequences of length n and m nucleotides respectively. At each Round of the game a player can remove a random number of nucleotides from one sequence or the same number of nucleotides from both sequences. The player who removes the last nucleotide wins.

arrays bioinformatics chromosomes computer-science fasta game loop nucleotides program python student

Last synced: 18 Aug 2025

https://github.com/arendsee/zwc

A fast version of the EMBOSS wordcount utility

bioinformatics fasta wordcount

Last synced: 26 Jan 2026

https://github.com/felselva/flfasta

Command-line application to filter sequences by length in FASTA files.

fasta

Last synced: 17 Jan 2026

https://github.com/vmikk/seqhasher

SeqHasher - A tool for hashing individual sequences in FASTA files

dna-sequences fasta fastq hashing

Last synced: 25 Jul 2025

https://github.com/jmjuanes/bedjs

Manage BED files with Node.JS (Bioinformatics)

bed bioinformatics fasta

Last synced: 31 Mar 2025

https://github.com/caleb-collar/motif-sniffer

Report, proposal, and mvp implementation of a simple tool for use in finding motifs in genome data. 🧬

bioinformatics fasta motif phage python

Last synced: 04 Apr 2025

https://github.com/robertopreste/allfreqs

Calculate allele frequencies from a sequence multialignment.

allele-frequencies bioinformatics csv fasta python

Last synced: 17 Jan 2026

https://github.com/pentalpha/alenhador

Parallel aligner (Needleman–Wunsch) for nucleotide sequences (.fasta) with similarity heuristic filter.

align-dna-sequences aligned-sequences alignment bioinformatics cpp cpp11 fasta heuristic-search heuristics nucleotide-sequences parallel-computing search

Last synced: 15 May 2026

https://github.com/abhijeetsingh1704/fasta2q

simple and convenient program to convert fasta sequences to fastq sequences

conversion fasta fasta-format fasta-sequences fastq fastq-files fastq-format fq sequence

Last synced: 19 Oct 2025

https://github.com/averissimo/mass-blast

Workflow to accelerate the annotation of unkown coding sequences

bioinformatics blast fasta

Last synced: 03 Apr 2025

https://github.com/scbirlab/bioino

đź’» Interconverting FASTA, GFF, and CSV.

bioinformatics fasta gff gff3 sequencing

Last synced: 23 Jan 2026

https://github.com/pprattis/chromosome-last-nucleotide-game

A Python script that implements a two player strategic game with two chromosomes having length n and m of nucleotides respectively. In each Round of the game a player can destroy one of the chromosomes and split the other into two non-empty parts. The player who deletes the last nucleotide wins.

arrays bioinformatics chromosomes computer-science fasta game loop nucleotides program python student

Last synced: 24 Oct 2025

https://github.com/jfjlaros/fastools

Various tools for the analysis and manipulation of FASTA and FASTQ files.

bioinformatics fasta fastq ngs

Last synced: 27 Feb 2026

https://github.com/se7en69/bio-wrangler

Bio-Wrangler is a Python package for bioinformatics data wrangling. It helps load, filter, merge, and summarize bioinformatics datasets from formats like FASTA, FASTQ, VCF, and GFF.

bio-wrangler bioinformatics development fasta fastq gff python pythonpackage vcf wrangler

Last synced: 06 Feb 2026

https://github.com/edawson/tinyfa

A header-only C++ FASTA parser and indexer

fasta genomics header-only

Last synced: 16 May 2026

https://github.com/bjeight/fastats

Very simple statistics from fasta files

bioinformatics fasta genomics

Last synced: 27 Feb 2026

https://github.com/abhijeetsingh1704/proteincleaner

a python utility to clean PROTEIN sequences and headers

convertion fasta genbank

Last synced: 21 Mar 2025