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@bge-barcoding BGE barcoding

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    13 repositories

    • fasta-cleaner

      Public
      Python
      •
      MIT License
      •1•0•3•1•Updated Jan 14, 2025Jan 14, 2025

    • ena-taxid-creation

      Public
      Generate ENA taxonomy request form for generation of new species-level taxonomic IDs
      Python
      •
      Apache License 2.0
      •1•1•0•0•Updated Jan 14, 2025Jan 14, 2025

    • MitoGeneExtractor-BGE

      Public
      The MitoGeneExtractor can be used to extract protein coding mitochondrial genes, such as COI and others from short and long read sequencing libraries.
      C++
      •
      GNU Affero General Public License v3.0
      •3•0•0•0•Updated Jan 13, 2025Jan 13, 2025

    • gene_fetch

      Public
      A Python tool for retrieving protein and/or gene sequences from NCBI databases. The script can fetch both protein and nucleotide sequences for a given gene across multiple taxa, with support for traversing taxonomic hierarchies when sequences aren't available at the given taxonomic level (dictated by input taxid).
      Python
      •
      MIT License
      •1•0•0•0•Updated Jan 3, 2025Jan 3, 2025

    • sample-processing

      Public
      Collection of scripts to download NCBI taxonomy, process BOLD-downloaded sample metadata, and generate necessary files for downstream processes.
      Python
      •
      Apache License 2.0
      •2•0•0•0•Updated Dec 18, 2024Dec 18, 2024

    • StayingMapped

      Public
      Mapping between different standards relevant to BGE
      Java
      •
      Apache License 2.0
      •1•1•3•0•Updated Oct 7, 2024Oct 7, 2024

    • ena-read-upload

      Public
      Collection of script to generate sample registration forms and bulk-ena-webincli spreadsheet for submission of reads to ENA.
      Python
      •1•0•0•0•Updated Sep 17, 2024Sep 17, 2024

    • barcode_validator

      Public
      Standardized validation of barcodes
      Python
      •
      Apache License 2.0
      •5•0•0•0•Updated Aug 31, 2024Aug 31, 2024

    • barcode-constrained-phylogeny

      Public
      Pipeline for building topologically-constrained phylogenies from DNA barcode data
      Python
      •
      Apache License 2.0
      •3•0•0•0•Updated Aug 23, 2024Aug 23, 2024

    • BOLDigger2_batch

      Public
      Preparation and batch submission of cox1 barcodes to BOLDigger2
      Shell
      •
      Apache License 2.0
      •1•0•0•0•Updated Aug 9, 2024Aug 9, 2024

    • bold-library-curation

      Public
      Perl
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated May 29, 2024May 29, 2024

    • skimming-review-mgmt

      Public
      Repository for aggregating and reviewing skimming runs
      Apache License 2.0
      •0•1•1•0•Updated May 22, 2024May 22, 2024

    • .github

      Public
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Jan 24, 2024Jan 24, 2024