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/torognes/vsearch

Versatile open-source tool for microbiome analysis

amplicon bioinformatics chimera clustering fasta fastq metabarcoding metagenomics microbiome search sequence-alignment

Last synced: 21 Oct 2025

https://github.com/bebop/poly

A Go package for engineering organisms.

alignment bioengineering bioinformatics codon-optimizer computational-biology dna dna-barcode dna-barcoding fasta genbank genetic-engineering go golden-gate mash molecular-biology plasmids primer-design sequence-hashing synbio synthetic-biology

Last synced: 05 May 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/seqan/seqan

SeqAn's official repository.

alignment bioinfomatics blast bwt cpp14 fasta fastq-format high-performance htslib indexing sam-bam seqan sequence-alignments simd suffixarray

Last synced: 15 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: 15 May 2025

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/biosyntax/biosyntax

Syntax highlighting for computational biology

bam bioinformatics computational-biology fasta gedit less pdb sublime-text syntax-highlighting vcf vim

Last synced: 07 Apr 2025

https://github.com/bioSyntax/bioSyntax

Syntax highlighting for computational biology

bam bioinformatics computational-biology fasta gedit less pdb sublime-text syntax-highlighting vcf vim

Last synced: 05 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: 15 May 2025

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: 15 Jul 2025

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: 21 Oct 2025

https://github.com/gabaldonlab/redundans

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

assembled-contigs assembly bioinformatics closing contigs docker-image fasta gap genome-assembly genomics heterozygous mate-pairs paired-end pipeline polymorphic python scaffolding

Last synced: 20 Aug 2025

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/muellan/metacache

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

bioinformatics bioinformatics-algorithms bioinformatics-tool classification dna-sequences fasta fastq genome genomic-data-analysis long-reads metagenomes metagenomic-analysis metagenomic-classification metagenomic-data metagenomics ncbi-refseq read-mapping refseq short-read-mapper taxonomy

Last synced: 09 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/biogenies/tidysq

tidy processing of biological sequences in R

bioconductor bioinformatics biological-sequences fasta r rstats s3 sequences tibble tidy tidyverse vctrs

Last synced: 18 Aug 2025

https://github.com/jfjlaros/demultiplex

Versatile FASTA/FASTQ demultiplexer.

demultiplex fasta fastq ngs

Last synced: 04 May 2025

https://github.com/jetbrains-research/bioinf-commons

Bioinformatics library in Kotlin

2bit bam bed bioinformatics cancellable chip-seq dataframe dataset dna-sequence fasta fastq hmm hypothesis-testing kotlin methylation mixture progress sampling

Last synced: 19 Oct 2025

https://github.com/koeng101/dnadesign

A Go package for designing DNA.

bioinformatics codon-optimization codon-usage computational-biology dna-barcode dna-folding fasta fastq genbank genetic-engineering go goldengate molecular-biology pileup plasmids rna-folding sam synbio synthetic-biology

Last synced: 13 Apr 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: 11 Mar 2025

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: 01 Oct 2025

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

A FASTA/FASTQ format parser library

fasta fastq

Last synced: 18 Aug 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/incertae-sedis/smof

Explore and analyze biological sequence data

bioinformatics biology fasta genomics sequence sequence-analysis

Last synced: 17 Dec 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/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/wurmlab/npsearch

NpSearch: Search for Neuropeptides

cleavage-sites fasta neuropeptides neuropeptides-precursor neuroscience ruby signal-peptides

Last synced: 24 Sep 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/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/ctskennerton/fxtract

Extract sequences from a fastx file given a subsequence or identifier

bioinformatics fasta fastq

Last synced: 21 Mar 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/wang-q/faops

faops operates fasta files

fasta kent-utilities klib

Last synced: 21 Jun 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/sing-group/seda

SEquence DAtaset builder

bioinformatics fasta fasta-sequences java sequence-dataset-builder sequences

Last synced: 03 Jul 2025

https://github.com/bunnysunny24/smart-agriculture

Smart Agriculture Using Sensors and Ai

arduino fasta firebase javascript mahine-learning matpl react sensors

Last synced: 30 Oct 2025

https://github.com/orangeSi/biokits

bioinformatics tools

bioinformatics fasta

Last synced: 10 Jul 2025

https://github.com/orangesi/biokits

bioinformatics tools

bioinformatics fasta

Last synced: 01 May 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/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: 04 Mar 2025

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

Protein Cleaver is a versatile tool for protein analysis and digestion.

digestion fasta mass-spectrometry peptide peptide-identification peptide-sequences peptides protein protein-sequences proteomics proteomics-data-analysis streamlit streamlit-cloud

Last synced: 15 Oct 2025

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/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/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/abhijeetsingh1704/dupremover

Removes duplicate sequences in multifasta file

fasta fasta-format fasta-sequences unique

Last synced: 17 Aug 2025

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: 14 Jul 2025

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/romgrk/bioinformatics-parser

Simple nodejs fasta/fastq parser

bioinformatics fasta fastq

Last synced: 14 Apr 2025

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/orangesi/pykits

simple python script for bioinformatics

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

Last synced: 28 Feb 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: 11 Dec 2025

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: 22 Feb 2025

https://github.com/biodasturchi/autodock4

Autodock 4 orqali ligand-oqsil mexanizmini ko'rish

fasta pdb pdbqt python shell

Last synced: 14 Mar 2025

https://github.com/jmjuanes/bedjs

Manage BED files with Node.JS (Bioinformatics)

bed bioinformatics fasta

Last synced: 31 Mar 2025

https://github.com/abhijeetsingh1704/proteincleaner

a python utility to clean PROTEIN sequences and headers

convertion fasta genbank

Last synced: 21 Mar 2025

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: 29 Jul 2025

https://github.com/edawson/tinyfa

A header-only C++ FASTA parser and indexer

fasta genomics header-only

Last synced: 25 Feb 2025

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: 15 Apr 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/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/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/mnsmar/rnadna

Convert sequence representation RNA - DNA for FASTA/Q

bioinformatics dna fasta fastq go rna

Last synced: 06 May 2025

https://github.com/tusharpandey003/fasta-sequence-analysis-web-app

Analysis of FASTA ,Protein,DNA sequence.

bioinformatics biotechnology data-science dna-sequence-analysis dna-sequences fasta fasta-sequence fasta-sequences nucleotide-sequence protein-sequences sequence-analysis streamlit web-application

Last synced: 13 Mar 2025

https://github.com/mdcjansen/dba

DNA barcoding analysis pipeline

ab1 bioinformatics bioinformatics-analysis blastn dna dna-alignment dna-barcode dna-barcoding dna-sequences fasta genbank genbank-files genomics mega11 phylogenetics phylogeny sanger-chromatograms species-identification

Last synced: 11 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/jfjlaros/fastools

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

bioinformatics fasta fastq ngs

Last synced: 22 Feb 2025

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/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/jistr/seq2fasta

Converts one or more DNA bare sequence files (.seq) into one FASTA format file (.fas).

converter dna fas fasta seq

Last synced: 06 Oct 2025

https://github.com/schlaubischlump/wormbase_fasta

Download all .genomic.fa.gz files from https://parasite.wormbase.org.

fasta ftp genome python python3 wormbase

Last synced: 29 Oct 2025

https://github.com/chrisarg/bio-seqalignment-components-sundry

Various components for building RNA sequencing applications in Perl

bioinformatics fasta fastq rna-seq sequence-alignment sequencing

Last synced: 26 Mar 2025

https://github.com/haha-systems/windowpain

Windowpain is a random-access tool for reading genetic sequences from huge FASTA sequence files in milliseconds.

dna fasta mmap rna zig

Last synced: 12 Nov 2025

https://github.com/ctskennerton/fx_tools

Very small utilities for interrogating fasta and fastq files

bioinformatics fasta fastq sequence-analysis

Last synced: 02 Apr 2025

https://github.com/alpaylan/sars

Suffix Array Library for Rust

fasta prefix-table suffix-array

Last synced: 24 Mar 2025

https://github.com/veupathdb/service-multi-blast

Async BLAST+ query service and supporting libraries.

blast fasta library ncbi ncbi-blast query service

Last synced: 06 Aug 2025

https://github.com/moold/fastat

Ultrafast to get statistics from fasta and fastq files

fasta fastq

Last synced: 18 Aug 2025

https://github.com/sgtpep/vimsa

The VIM-based multiple sequence alignment (MSA) editor.

bioinformatics fasta msa sequence-alignment vim

Last synced: 20 Mar 2025

https://github.com/engkinandatama/ncbi-sequence-fetcher

NCBI Sequence Fetcher is a Python desktop app for downloading nucleotide sequences and extracting metadata from NCBI. It features an easy-to-use GUI, supports FASTA and GenBank formats, and helps researchers students and bioinformaticians efficiently collect DNA sequences and store metadata in Excel files.

academic bioinformatics bioinformatics-tool data-scraping fasta genbank metadata metadata-extraction molecular-biology ncbi nucleotide-sequences python tkinter