mkCOInr - Make and customize COInr, a comprehensive COI database form NCBI-nucleotide and BOLD

mkCOInr is a series of Perl scripts that aims to create COInr, a comprehensive COI database form NCBI-nucleotide and BOLD and customize it.

If you use mkCOInr in scientific works, please cite the following article:

Meglécz, E. 2023. COInr and mkCOInr: Building and customizing a non-redundant barcoding reference database from BOLD and NCBI using a semi-automated pipeline. Molecular Ecology Resources, 21, 933-945

Table of Contents

• Overview of mkCOInr
• Installation
  • Third-party programs
  • mkCOInr scripts
• Run mkCOInr
• Tutorial
  • Customize database
    • Download and untar COInr
    • Add custom sequences to a database
    • Select sequences from existing database
    • Select region
    • Format database
    • Chaining steps to make a custom database
  • Create COInr from BOLD and NCBI
    • Download NCBI taxonomy
    • NCBI sequences
    • BOLD sequences
    • Pool and dereplicate datasets
• Description
  • add_taxids.pl
    • Aim
    • Input files
    • Parameters/options
    • Algorithm
    • Output
  • dereplicate.pl
    • Aim
    • Input files
    • Parameters/options
    • Algorithm
    • Output
  • download_bold.pl
    • Aim
    • Input files
    • Parameters/options
    • Algorithm
    • Output
  • download_taxonomy.pl
    • Aim
    • Input
    • Parameters/options
    • Algorithm
    • Output
  • format_bold.pl
    • Aim
    • Input files
    • Parameters/options
    • Algorithm
    • Output
  • format_bold_package.pl
    • Aim
    • Input files
    • Parameters/options
    • Algorithm
    • Output
  • format_custom.pl
    • Aim
    • Input
    • Parameters/options
    • Algorithm
    • Output
  • format_db.pl
    • Aim
    • Input
    • Parameters/options
    • Algorithm
    • Output
  • format_rdp.pl
    • Aim
    • Input files
    • Parameters/options
    • Algorithm
    • Output
  • format_ncbi.pl
    • Aim
    • Input files
    • Parameters/options
    • Algorithm
    • Output
  • get_subtaxa.pl
    • Aim
    • Input files
    • Parameters/options
    • Algorithm
    • Output
  • pool_and_dereplicate.pl
    • Aim
    • Input files
    • Parameters/options
    • Algorithm
    • Output
  • reduce_metadata.pl
    • Aim
    • Input files
    • Algorithm
    • Output
  • select_region.pl
    • Aim
    • Input files
    • Parameters/options
    • Algorithm
    • Output
  • select_taxa.pl
    • Aim
    • Input files
    • Parameters/options
    • Algorithm
    • Output
• Input/Output
  • Taxonomy related files or directories
    • ncbitax_dir
    • taxonomy
    • RDP classifier taxid file
    • taxon_list
  • Lineage files
    • BOLD data package TSV
    • lineage tsv without taxID
    • lineage tsv with taxID (output of select_taxa.pl)
    • lineage tsv with taxID (output of add_taxids.pl)
    • custom lineages tsv
    • ambiguous lineages
  • Sequence files
    • sequence tsv without taxID
    • sequence tsv with taxID
    • custom sequences tsv
    • RDP classifier trainset fasta
  • Database formats
    • BLAST database files
    • full tsv
    • QIIME
    • RDP
    • SINTAX
    • VTAM database files
  • Other
    • outdir
    • out
• Glossary
  • ranked lineage
  • seqID
  • taxID
  • taxlevel index
• List of References
• Citation
• Change Log

Indices and tables

• Index

• Module Index

• Search Page