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ncbi-genome-download kblin

175

956

apache-2.0

35

Scripts to download genomes from the NCBI FTP servers

ncbi python biology genbank genomics command-line bioinformatics download-genomes

Created 2016-05-03

303 commits to master branch, last one 3 months ago

poly bebop

73

676

mit

13

A Go package for engineering organisms.

Created 2020-05-29

491 commits to main branch, last one about a month ago

DnaFeaturesViewer Edinburgh-Genome-Foundry

92

599

mit

19

:eye: Python library to plot DNA sequence features (e.g. from Genbank files)

genbank visualization bioinformatics dna-visualization molecular-biology synthetic-biology

Created 2016-09-20

183 commits to master branch, last one about a year ago

pyGenomeViz moshi4

23

284

mit

3

A genome visualization python package for comparative genomics

gff gff3 python genbank synteny genomics matplotlib microbiology visualization bioinformatics microbial-genomics comparative-genomics genomics-visualization

Created 2022-05-20

416 commits to main branch, last one 22 days ago

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

genome_updater pirovc

15

146

mit

1

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

bash ncbi genome refseq genbank genomes database download genomics sequence bioinformatics

Created 2017-05-11

164 commits to master branch, last one 10 months ago

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

ganon pirovc

13

87

mit

4

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierar...

gtdb ncbi k-mer refseq genbank taxonomy microbiome minimizers bloom-filter metagenomics bioinformatics

Created 2018-08-30

690 commits to master branch, last one 9 months ago

Cenote-Taker2 mtisza1

7

55

mit

2

Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)

virus virome genbank hhblits hallmark hhsearch prophage discovery annotation metagenomes cenote-taker2 virus-discovery virus-evolution virus-sequences prophage-prediction cenote-unlimited-breadsticks

Created 2019-09-12

337 commits to master branch, last one 10 months ago

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

mpox nextstrain

19

45

mit

18

Nextstrain build for mpox virus

mpox augur auspice genbank metadata pathogen pipeline monkeypox nextstrain phylogenetics bioinformatics virus-evolution genomic-epidemiology

Created 2022-05-19

907 commits to master branch, last one 16 hours ago

multiSub maximilianh

2

35

gpl-3.0

4

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...

ena tsv ncbi fasta genbank ncbi-ftp sarscov2 meta-data gisaid-xls sars-cov-2 gisaid-format gisaid-upload gisaid-uploader

Created 2021-04-02

74 commits to stable branch, last one 2 years ago

dnadesign Koeng101

0

26

other

4

A Go package for designing DNA.

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

Created 2023-12-07

548 commits to main branch, last one about a month ago