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.

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

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

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

VAPiD: Viral Annotation and Identification Pipeline

Nextstrain build for mpox virus

Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories

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

A Go package for designing DNA.

🧬 💻 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

An automated pipeline for retrieving orthologous DNA sequences from GenBank in R