OBITools4 Documentation

Welcome obitools4

About Installation OBITools principles The OBITools commands Full documentation Cookbook Contribute to the doc

OBITools4 are a suite of UNIX command-line tools for processing DNA metabarcoding data, developed at LECA ( University of Grenoble). Following the philosophy of standard UNIX tools such as grep, uniq or wc, each command performs a single, well-defined operation on sequence records, and is fully parameterisable by a large set of options. Written in Go, OBITools4 take full advantage of modern multi-core architectures to handle the large datasets produced by today’s high-throughput sequencers. Rather than imposing a fixed pipeline, OBITools4 provide the building blocks that let you compose your own analysis workflow tailored to your biological questions.

Commands overview #

Basics #

CommandDescription
obiannotateAdds, deletes, or modifies annotations, identifiers, and sequences.
obicomplementComputes the reverse complement of every sequence.
obiconvertConverts sequence files between bioinformatics formats (FASTA, FASTQ, JSON…).
obicountCounts sequence records, reporting variants, reads, and total nucleotides.
obicsvConverts sequence datasets into CSV format.
obidemergeReverses obiuniq merging by expanding each merged entry into individual sequences.
obidistributeSplits sequences into multiple output files based on annotations or hash sharding.
obigrepFilters sequences based on ID, annotations, sequence content, length, or taxonomy.
obijoinEnriches a sequence dataset with annotations imported from a secondary file.
obimatrixBuilds a sample × sequence count matrix (OTU table) from annotated sequences.
obisummaryProvides a statistical overview of a sequence dataset.
obiuniqDereplicates sequences, grouping identical sequences and recording their abundance.

Demultiplexing #

CommandDescription
obimultiplexDemultiplexes sequencing reads by identifying sample-specific tags and primers.
obitagpcrDemultiplexes paired-end reads by assigning them to samples based on primers and barcodes.

Alignments #

CommandDescription
obicleanDenoises PCR-amplified sequences by filtering out most of the spurious and chimeric sequences.
obipcrPerforms in silico PCR, returning amplicon sequences for given primer pairs.
obipairingAligns forward and reverse paired-end reads into full-length amplicons.
obitagAssigns taxonomic annotations by searching a reference database with LCA inference.

Taxonomy #

CommandDescription
obitaxonomyLoads, inspects, and queries a taxonomy database.

Advanced #

CommandDescription
obiscriptApplies custom Lua scripts to process sequence records with full programmable logic.

Others #

CommandDescription
obimicrosatScans DNA sequences for simple sequence repeats (microsatellites).
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