OBITools scripts

• Metabarcode design and quality assessment
  • ecoPCR: in silico PCR
  • ecoPrimers: new barcode markers and primers
  • ecotaxstat : getting the coverage of an ecoPCR output compared to the original ecoPCR database
  • ecotaxspecificity: Evaluates barcode resolution
• File format conversions
  • obiconvert: converts sequence files to different output formats
  • obipr2: converts silva database into an ecoPCR database
  • obisilva: converts silva database into an ecoPCR database
  • obitaxonomy: manages taxonomic databases
  • obitab: converts a sequence file to a tabular file
• Sequence annotations
  • ecotag: assigns sequences to taxa
  • obiannotate: adds/edits sequence record annotations
  • obiaddtaxids: adds taxids to sequence records using an ecopcr database
• Computations on sequences
  • illuminapairedend: aligns paired-end Illumina reads
  • ngsfilter : Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers
  • obicomplement: reverse-complements sequences
  • obiclean: tags a set of sequences for PCR/sequencing errors identification
  • obicut: trims sequences
  • obijoinpairedend: Joins paired-end reads
  • obiuniq: groups and dereplicates sequences
• Sequence sampling and filtering
  • obiextract: extract samples from a dataset
  • obigrep: filters sequence file
  • obihead: extracts the first sequence records
  • obisample: randomly resamples sequence records
  • obiselect : selects representative sequence records
  • obisplit: Splits a sequence file in a set of subfiles
  • obisubset specific options
  • Options to specify input format
  • Options to specify output format
  • Common options
  • obisubset modifies sequence attributes
  • obisubset used sequence attribute
  • obitail: extracts the last sequence records
• Statistics over sequence file
  • ecodbtaxstat: gives taxonomic rank frequency of a given ecopcr database
  • obicount: counts the number of sequence records
  • obistat: computes basic statistics for attribute values
• Utilities
  • oligotag: Designs a set of oligonucleotides with specified properties
  • obidistribute: Distributes sequence records over several sequence records files
  • obisort: Sorts sequence records according to the value of a given attribute
  • obitaxonomy: manages taxonomic databases
  • ecofind: querying a taxonomic database