genbank

Scripts to download genomes from the NCBI FTP servers

A Go package for engineering organisms.

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

A genome visualization python package for comparative genomics

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.

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.

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

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

VAPiD: Viral Annotation and Identification Pipeline

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

Nextstrain build for mpox virus

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.

A lua package for designing DNA.

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.

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.

An example GenBank file reader in Rust

👓 Python library to parse Snapgene *.dna files to dict or biopython seqrecord.

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

😴 📂 Create and Query a Local Copy of GenBank in R

a toolbox for utilize organelle genomic data