{"repo":"pirovc/genome_updater","free":true,"listed":false,"github":"https://github.com/pirovc/genome_updater","clone":"git clone https://github.com/pirovc/genome_updater.git","description":"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.","language":"Shell","stars":172,"topics":["bioinformatics","ncbi","bash","genome","sequence","refseq","genbank","download","database","genomes"],"license":"MIT","category":"databases-storage","readme_excerpt":"genome updater genome updater is a bash script that downloads and updates (non-redundant) snapshots of the NCBI Genomes repository (RefSeq/GenBank) [1] with advanced filters, detailed logs and reports, file integrity checks (MD5, gzip), NCBI taxonomy and GTDB [2] integration and support for parallel [3] downloads. genome updater uses the assembly summary.txt to retrieve data. Quick usage guide Download Update Some time later, get a up-to-date version from NCBI, downloading only newly added files: - boolean flags (e.g. -G ) are not tracked between versions and have to be repeated on the update command to be included. Installation conda/mamba direct file download - bash =4. or above is required. - this script attempts to be portable and only depends on GNU Core Utilities + few additional tools ( awk bc find fmt gzip join md5sum parallel sed tar wget and optionally curl ) which are commonly available and installed in most distributions. - genome updater.sh -Z will show more info about dependencies in your system and report if someting is missing - To test if all genome updater functions are running properly on your system: Parameters Details on local updates When updating an existing local repository: - Newly added sequences will be downloaded, creating a new version. - -b can be used to change the version name, otherwise will use the current timestamp by default. - Removed or old sequences will be retained, but not transferred to the new version. - Repeated/unchanged files are ","default_branch":null,"files":null,"tree":[],"storefront":"/r/pirovc","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/pirovc/genome_updater/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}