fasta

There are 4 repositories under fasta topic.

shenwei356 / seqkit
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
bioinformatics cross-platform fasta golang sequence toolkit fastq tool manipulation
Language:Go 1478
torognes / vsearch
Versatile open-source tool for microbiome analysis
amplicon bioinformatics chimera clustering fasta fastq metabarcoding metagenomics microbiome search sequence-alignment
Language:C++ 723
poly
bebop / poly
A Go package for engineering organisms.
synthetic-biology synbio genetic-engineering molecular-biology bioengineering computational-biology bioinformatics dna fasta genbank codon-optimizer sequence-hashing plasmids primer-design dna-barcode dna-barcoding golden-gate mash alignment go
Language:Go 711
epam / ketcher
Web-based molecule sketcher
cdx cdxml cheminformatics chemistry cml lifescience molecule molecule-editor nucleotide-sequence nucleotides peptides smarts smiles helm amino-acid-sequence amino-acids fasta idt molfile mdl-molfile
Language:TypeScript 673
jupyterlab / jupyter-renderers
Renderers and renderer extensions for JupyterLab
jupyterlab plotly geojson katex fasta vega vega-lite jupyterlab-extension
Language:HTML 510
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
Language:C++ 497
mdshw5 / pyfaidx
Efficient pythonic random access to fasta subsequences
python bioinformatics fasta indexing dna protein genomics bgzf samtools
Language:Python 479
seqan3
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
Language:C++ 437
edgardomortiz / vcf2phylip
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
vcf snps phylip alignment phylogenetics nexus binary snapp fasta outgroup convert-snps vcf-files phylogenetic-analysis vcf-format phylip-matrix haploid diploid polyploid
Language:Python 320
lmdu / pyfastx
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
fasta python biology dna genome assembly sequence fastq bioinformatics
Language:C 290
samtools / htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
genomics sequencing dna ngs bam cram sam fasta vcf java-api java
Language:Java 290
bioSyntax / bioSyntax
Syntax highlighting for computational biology
bioinformatics computational-biology syntax-highlighting less vim gedit sublime-text bam vcf fasta pdb
Language:Shell 269
mbhall88 / rasusa
Randomly subsample sequencing reads or alignments
bioinformatics fastq subsampling coverage fasta genome-analysis random downsample rust alignment bam
Language:Rust 245
genomics
igordot / genomics
A collection of scripts and notes related to genomics and bioinformatics
bioinformatics genomics sequencing illumina fasta fastq gtf vcf nanopore dna science workflow fast5
Language:R 217
pydna
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
Language:Python 207
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
genomics compression fastq vcf bam sam fasta gvf 23andme gzip bgzip samtools bwa cram
Language:C 171
DNAnalyzer
VerisimilitudeX / DNAnalyzer
Precision genomics for everyone, everywhere. Powered by private AI.
artificial-intelligence bioinformatics biotechnology cli computational-biology dna-analysis dna-sequencing fasta genomics machine-learning on-device open-source precision-medicine privacy regulatory-elements
Language:Java 165
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
Language:C++ 161
torognes / swarm
A robust and fast clustering method for amplicon-based studies
bioinformatics clustering fasta metabarcoding microbiome sequence
Language:C++ 138
eead-csic-compbio / get_homologues
GET_HOMOLOGUES: a versatile software package for pan-genome analysis
pangenome bacteria annotation plants transcriptome clustering fasta genbank pangene
Language:Perl 121
seqfu2
telatin / seqfu2
:rocket: seqfu - Sequece Fastx Utilities
fastq fasta bioinformatics bioinformatics-tool bioconda genomics ngs sequencing
Language:Nim 121
smaegol / PlasFlow
Software for prediction of plasmid sequences in metagenomic assemblies
classification prediction contigs plasmid fasta plasmid-sequences tensorflow metagenome-assembly metagenome metagenomes plasmids plasflow
Language:Python 105
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
Language:Clojure 92
evolbioinfo / goalign
Goalign is a set of command line tools and an API to manipulate multiple sequence alignments. It is implemented in Go language.
phylogeny alignment phylip fasta phylip-alignment nexus
Language:Go 87
markschl / seq_io
FASTA and FASTQ parsing in Rust
fasta fastq fastx parser rust
Language:Rust 78
josiahseaman / FluentDNA
FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.
alignment bioinformatics bioinformatics-tool chain-alignment ddv dna fasta fasta-sequences fluent fluentdna liftover msa protein sequencing visualization
Language:JavaScript 70
BioJulia / FASTX.jl
Parse and process FASTA and FASTQ formatted files of biological sequences.
fasta bio biojulia julia parsing file-format fastq fastq-format fastq-files fasta-format fasta-files
Language:Julia 66
muellan / metacache
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
genome read-mapping refseq taxonomy metagenomics metagenomic-analysis metagenomic-classification metagenomes metagenomic-data ncbi-refseq fasta fastq dna-sequences genomic-data-analysis classification bioinformatics bioinformatics-tool bioinformatics-algorithms short-read-mapper long-reads
Language:C++ 64
KirillKryukov / naf
Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences
compression dna fasta fastq file-format protein rna
Language:C 59
sbslee / fuc
Frequently used commands in bioinformatics
api bam bed bioinformatics cli cram fasta fastq gff gtf maf sam vcf visualization
Language:Python 56
cartoonist / kseqpp
Fast FASTA/Q parser and writer (C++ re-implementation of kseq library)
fasta fasta-files fastq fastq-files parser writer
Language:C++ 54
rcs333 / VAPiD
VAPiD: Viral Annotation and Identification Pipeline
virus annotations genbank bioinformatics virology biology ngs fasta metadata ncbi
Language:Shell 54
brentp / hts-python
pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)
genomics python htslib bioinformatics bam sam fasta
Language:Python 49
OpenGene / UniqueKMER
Generate unique KMERs for every contig in a FASTA file
unique kmer sequencing bioinformatics ngs virus fasta
Language:C 48
tidysq
BioGenies / tidysq
tidy processing of biological sequences in R
biological-sequences rstats bioinformatics tidyverse r tidy bioconductor fasta sequences tibble vctrs s3
Language:C++ 44
maximilianh / multiSub
Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input directory and merges everything into a single output directory. Auto-detects input file formats. Can submit the results to multiple repositories from the command line.
sarscov2 sars-cov-2 gisaid-format gisaid-upload gisaid-xls ncbi-ftp genbank tsv ena meta-data fasta gisaid-uploader ncbi
Language:Python 36