32 results found Sort:

shenwei356
seqkit shenwei356
160
1.3k
mit
27
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
tool fasta fastq golang toolkit sequence manipulation bioinformatics cross-platform
Created 2016-02-28
819 commits to master branch, last one 18 days ago
bebop
poly bebop
73
676
mit
13
A Go package for engineering organisms.
go dna mash fasta synbio genbank plasmids alignment dna-barcode golden-gate dna-barcoding primer-design bioengineering bioinformatics codon-optimizer sequence-hashing molecular-biology synthetic-biology genetic-engineering computational-biology
Created 2020-05-29
491 commits to main branch, last one about a month ago
torognes
vsearch torognes
125
671
other
43
Versatile open-source tool for microbiome analysis
fasta fastq search chimera amplicon clustering microbiome metagenomics metabarcoding bioinformatics sequence-alignment
Created 2014-05-16
3,288 commits to master branch, last one 2 days ago
jupyterlab
jupyter-renderers jupyterlab
78
490
bsd-3-clause
29
Renderers and renderer extensions for JupyterLab
vega fasta katex plotly geojson vega-lite jupyterlab jupyterlab-extension
Created 2017-06-08
629 commits to main branch, last one 5 months ago
seqan
seqan seqan
171
483
other
42
SeqAn's official repository.
bwt simd blast cpp14 fasta seqan htslib sam-bam indexing alignment suffixarray fastq-format bioinfomatics high-performance sequence-alignments
Created 2012-10-25
8,347 commits to main branch, last one 7 days ago
mdshw5
pyfaidx mdshw5
75
460
other
9
Efficient pythonic random access to fasta subsequences
dna bgzf fasta python protein genomics indexing samtools bioinformatics
Created 2013-09-12
879 commits to master branch, last one about a month ago
seqan
seqan3 seqan
82
410
other
25
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
blast cpp20 fasta fastq seqan modern fm-index samtools cpp-concepts bioinformatics sequence-analysis sequence-alignment
Created 2016-04-04
6,794 commits to main branch, last one a day ago
edgardomortiz
vcf2phylip edgardomortiz
85
294
gpl-3.0
9
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
vcf snps fasta nexus snapp binary phylip diploid haploid outgroup alignment polyploid vcf-files vcf-format convert-snps phylip-matrix phylogenetics phylogenetic-analysis
Created 2017-10-10
102 commits to master branch, last one about a year ago
samtools
htsjdk samtools
243
285
unknown
50
A Java API for high-throughput sequencing data (HTS) formats.
bam dna ngs sam vcf cram java fasta genomics java-api sequencing
Created 2014-04-29
2,848 commits to master branch, last one 22 days ago
lmdu
pyfastx lmdu
23
268
mit
7
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
dna fasta fastq genome python biology assembly sequence bioinformatics
Created 2019-03-19
606 commits to master branch, last one 4 months ago
bioSyntax
bioSyntax bioSyntax
30
255
gpl-3.0
17
Syntax highlighting for computational biology
bam pdb vcf vim less fasta gedit sublime-text bioinformatics syntax-highlighting computational-biology
Created 2017-12-05
188 commits to master branch, last one 3 years ago
mbhall88
rasusa mbhall88
17
212
mit
6
Randomly subsample sequencing reads or alignments
bam rust fasta fastq random coverage alignment downsample subsampling bioinformatics genome-analysis
Created 2019-09-26
240 commits to main branch, last one 2 months ago
igordot
genomics igordot
54
200
unknown
7
A collection of scripts and notes related to genomics and bioinformatics
dna gtf vcf fast5 fasta fastq science genomics illumina nanopore workflow sequencing bioinformatics
Created 2015-12-22
118 commits to master branch, last one 14 days ago
BjornFJohansson
pydna BjornFJohansson
45
166
other
13
Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.
dna gel fasta pydna python biology genbank jupyter anaconda biopython simulation bioinformatics gel-simulation gibson-assembly jupyter-notebook jupyter-notebooks cloning-strategies assembly-strategies gel-electrophoresis
Created 2015-02-04
1,738 commits to master branch, last one 11 days ago
divonlan
genozip divonlan
12
158
other
1
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
bam bwa gvf sam vcf cram gzip bgzip fasta fastq 23andme genomics samtools compression
Created 2019-12-15
3,261 commits to master branch, last one about a month ago
Gabaldonlab
redundans Gabaldonlab
20
130
gpl-3.0
8
Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
gap fasta python closing contigs assembly genomics pipeline mate-pairs paired-end polymorphic scaffolding docker-image heterozygous bioinformatics genome-assembly assembled-contigs
Created 2015-04-07
582 commits to master branch, last one 11 months ago
torognes
swarm torognes
23
127
agpl-3.0
14
A robust and fast clustering method for amplicon-based studies
fasta sequence clustering microbiome metabarcoding bioinformatics
Created 2012-11-10
2,935 commits to master branch, last one 7 months ago
telatin
seqfu2 telatin
7
112
gpl-3.0
3
:rocket: seqfu - Sequece Fastx Utilities
ngs fasta fastq bioconda genomics sequencing bioinformatics bioinformatics-tool
Created 2020-11-26
593 commits to main branch, last one 5 days ago
eead-csic-compbio
get_homologues eead-csic-compbio
26
110
other
17
GET_HOMOLOGUES: a versatile software package for pan-genome analysis
fasta plants genbank pangene bacteria pangenome annotation clustering transcriptome
Created 2015-11-26
592 commits to master branch, last one 6 days ago
smaegol
PlasFlow smaegol
28
98
gpl-3.0
8
Software for prediction of plasmid sequences in metagenomic assemblies
fasta contigs plasmid plasflow plasmids metagenome prediction tensorflow metagenomes classification plasmid-sequences metagenome-assembly
Created 2017-01-12
89 commits to master branch, last one 3 years ago
chrovis
cljam chrovis
12
90
apache-2.0
11
A DNA Sequence Alignment/Map (SAM) library for Clojure
bam bcf bed gff sam vcf wig 2bit cram fasta fastq bigwig clojure genomics bioinformatics
Created 2014-01-08
1,631 commits to master branch, last one 3 days ago
evolbioinfo
goalign evolbioinfo
8
73
gpl-2.0
13
Goalign is a set of command line tools and an API to manipulate multiple sequence alignments. It is implemented in Go language.
fasta nexus phylip alignment phylogeny phylip-alignment
Created 2016-08-24
645 commits to master branch, last one 2 months ago
markschl
seq_io markschl
11
72
mit
5
FASTA and FASTQ parsing in Rust
rust fasta fastq fastx parser
Created 2017-07-31
123 commits to main branch, last one about a year ago
josiahseaman
FluentDNA josiahseaman
7
65
unknown
8
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 bioinfo...
ddv dna msa fasta fluent protein liftover alignment fluentdna sequencing visualization bioinformatics chain-alignment fasta-sequences bioinformatics-tool
Created 2016-03-02
533 commits to python-master branch, last one 3 years ago
BioJulia
FASTX.jl BioJulia
20
62
mit
9
Parse and process FASTA and FASTQ formatted files of biological sequences.
bio fasta fastq julia parsing biojulia fasta-files fastq-files file-format fasta-format fastq-format
Created 2018-10-05
128 commits to master branch, last one 29 days ago
muellan
metacache muellan
11
57
gpl-3.0
7
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
fasta fastq genome refseq taxonomy long-reads metagenomes ncbi-refseq metagenomics read-mapping dna-sequences bioinformatics classification metagenomic-data short-read-mapper bioinformatics-tool metagenomic-analysis genomic-data-analysis bioinformatics-algorithms metagenomic-classification
Created 2017-02-07
1,029 commits to master branch, last one about a month ago
KirillKryukov
naf KirillKryukov
6
56
zlib
4
Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences
dna rna fasta fastq protein compression file-format
Created 2018-12-11
226 commits to master branch, last one 2 years ago
rcs333
VAPiD rcs333
15
51
mit
4
VAPiD: Viral Annotation and Identification Pipeline
ngs ncbi fasta virus biology genbank metadata virology annotations bioinformatics
Created 2016-12-15
355 commits to master branch, last one 3 years ago
sbslee
fuc sbslee
5
48
mit
1
Frequently used commands in bioinformatics
api bam bed cli gff gtf maf sam vcf cram fasta fastq visualization bioinformatics
Created 2021-03-26
952 commits to main branch, last one 5 months ago
OpenGene
UniqueKMER OpenGene
8
43
mit
11
Generate unique KMERs for every contig in a FASTA file
ngs kmer fasta virus unique sequencing bioinformatics
Created 2020-04-24
43 commits to master branch, last one 2 years ago