Scripts to download genomes from the NCBI FTP servers
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Apr 7, 2026 - Python
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genbank
Here are 109 public repositories matching this topic...
A Go package for engineering organisms.
go bioinformatics synthetic-biology computational-biology dna genbank alignment fasta molecular-biology mash synbio bioengineering primer-design golden-gate dna-barcode plasmids dna-barcoding codon-optimizer genetic-engineering sequence-hashing
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Jun 10, 2026 - Go
👁️ Python library to plot DNA sequence features (e.g. from Genbank files)
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Jul 2, 2025 - Python
A genome visualization python package for comparative genomics
visualization python bioinformatics genomics gff3 genbank matplotlib microbial-genomics microbiology comparative-genomics synteny genomics-visualization gff
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Jun 14, 2026 - Python
Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.
python bioinformatics jupyter anaconda simulation biology jupyter-notebook dna biopython genbank gel fasta jupyter-notebooks pydna gel-simulation gibson-assembly cloning-strategies gel-electrophoresis assembly-strategies
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Jul 29, 2026 - Python
genome_updater is a bash script that downloads and updates (non-redundant) snapshots of the NCBI Genomes repository (RefSeq/GenBank) with advanced filters, detailed logs and reports, file integrity checks, NCBI taxonomy and GTDB integration and support for parallel downloads.
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Jul 6, 2026 - Shell
GET_HOMOLOGUES: a versatile software package for pan-genome analysis
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Feb 13, 2026 - Perl
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 hierarchical classification, customized reporting and more
bioinformatics taxonomy bloom-filter metagenomics genbank microbiome k-mer ncbi refseq minimizers gtdb
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Jul 20, 2026 - Python
VAPiD: Viral Annotation and Identification Pipeline
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May 29, 2024 - Shell
Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)
virus annotation discovery genbank hhblits hhsearch metagenomes virome virus-discovery prophage hallmark virus-evolution cenote-taker2 prophage-prediction virus-sequences cenote-unlimited-breadsticks
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Jan 19, 2024 - Shell
Nextstrain build for mpox virus
metadata bioinformatics pipeline pathogen phylogenetics genbank augur nextstrain auspice virus-evolution genomic-epidemiology monkeypox mpox
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Jul 30, 2026 - Python
An AI-native molecular biology workbench for Claude Science: Claude opens sequence files and prepares analyses on request; you annotate, align, and review them in an interactive workspace.
bioinformatics mcp synthetic-biology computational-biology genbank crispr pcr plasmid molecular-biology sequence-alignment ai-agents claude primer-design sequence-analysis multiple-sequence-alignment bioinformatics-tool sanger-sequencing model-context-protocol mcp-app claude-science
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Jul 29, 2026 - TypeScript
Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
bioinformatics-pipeline genbank ncbi-submission ncbi-genbank cdc sra ncbi-sra ncbi-biosamples gisaid gisaid-uploader biosample gisaid-format gisaid-upload seqsender ncird ncird-id cdc-influenza-division
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Feb 20, 2026 - Python
A lua package for designing DNA.
go bioinformatics synthetic-biology computational-biology sam genbank fasta fastq molecular-biology synbio rna-folding goldengate dna-barcode plasmids codon-optimization codon-usage pileup genetic-engineering dna-folding
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Jul 8, 2026 - Go
A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.
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Jul 23, 2026 - Python
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.
tsv genbank fasta ncbi meta-data ena sars-cov-2 sarscov2 gisaid-uploader gisaid-format gisaid-upload gisaid-xls ncbi-ftp
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May 1, 2022 - Python
👓 Python library to parse Snapgene *.dna files to dict or biopython seqrecord.
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May 10, 2025 - Python
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