OBIKmers/obikmer
1
0 Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 34 Wiki Activity
Page: usage unitig
Pages
Home architecture formats index_layout installation theory encoding theory entropy_filter theory indexing_architecture theory kmer_indexing encoding theory kmer_indexing entropy_filter theory kmer_indexing indexing_architecture theory kmer_indexing kmers theory kmer_indexing minimizer_selection theory kmer_indexing superkmers theory kmers_and_superkmers theory minimizer_selection theory phylogeny kmer_based distance_metrics theory phylogeny kmer_based kmer_set_distances theory phylogeny snp_based central_snp_model theory phylogeny snp_based gamma_rate_heterogeneity theory phylogeny snp_based sampling_design theory phylogeny snp_based sankoff_model usage annotate usage convert usage dump usage estimate usage filter usage index_command usage merge usage pack usage phylo usage predicates usage query usage select usage superkmer usage unitig usage utils
Clone
4
usage unitig
Eric Coissac edited this page 2026-09-12 14:00:23 +02:00
Table of Contents

unitig

Dump the unitigs of an index as FASTA. A unitig is a maximal non-branching path through the de Bruijn graph implied by the index's kmers; the concatenation of every unitig reconstructs every stored kmer exactly once.

obikmer unitig INDEX [OPTIONS]

Arguments

Argument Description
INDEX Index directory

Options

unitig accepts the shared predicate options (--ingroup, --outgroup, --min-count, etc.) to restrict which kmers are included before the unitigs are enumerated.

Output is FASTA on stdout.

Wiki sidebar

Theory

Kmer indexing

Phylogeny

Kmer-based

SNP-based

Usage

Formats