ktGetLCA - explore hierarchical metagenomic data with zoomable pie
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Description:
- Computes the lowest common ancestor for accessions or taxonomy IDs (as
arguments or from <stdin>). If an input is a number, it is assumed
to be a taxonomy ID; otherwise it will be considered an accession or
sequence ID containing an accession in the fourth field of pipe notation
(e.g. "gi|12345|xx|ABC123.1|", ignoring fasta/fastq tag markers
[>,@]). If using <stdin>, the LCA can be computed for the first
fields of all input lines (default), or per input line, separated by
whitespace (see -s).
Usage:
- ktGetLCA [options] [acc/tax_ID ...] [< acc/taxID_list] > LCA
- -s
- Streaming mode. Each line is expected to be a whitespace-separated list of
inputs for a single lowest common ancestor computation. Taxonomy will be
preloaded, allowing for faster computation after a small upfront
time.