Annotation Parameters

Argument list, definitions and default values for hundo annotate:

Argument	Type or Choice	Description	Default
--prefilter-file-size	INTEGER	Any FASTQ file size smaller than this in bytes is omitted from being processed.	100000
--jobs	INTEGER	Use at most this many cores in parallel. The total running tasks at any given time will be jobs divided by threads.	auto
--out-dir	TEXT	Results output directory.	current directory
--no-conda		Do not use conda environments. Requires that all dependencies are installed and executable.	FALSE
--dryrun		Do not execute anything, just show the commands that will be executed by Snakemake.	FALSE
--author	TEXT	Will show in footer of summary HTML document.	uname
--aligner	[blast|vsearch]	local aligner; blast is more sensitive while vsearch is much faster	blast
--threads	INTEGER	When a step is multi-threaded, use this many threads. This is all or a subset of --jobs.	8
--database-dir	TEXT	Directory containing reference data or new directory into which to download reference data.	‘references’
--filter-adapters	TEXT	File path to adapters FASTA to use for trimming read ends.	None
--filter-contaminants	TEXT	File path to FASTA to use for filtering reads.	None
--allowable-kmer-mismatches	INTEGER	Kmer mismatches allowed during adapter trim process.	1
--reference-kmer-match-length	INTEGER	Length of kmer to search against contaminant sequences.	27
--reduced-kmer-min	INTEGER	Look for shorter kmers at read tips down to this length; 0 disables.	8
--minimum-passing-read-length	INTEGER	Passing single-end read length prior to merging.	100
--minimum-base-quality	INTEGER	Regions with average quality below this will be trimmed.	10
--minimum-merge-length	INTEGER	Minimum allowable read length after merging.	150
--allow-merge-stagger		Allow merging of staggered reads by VSEARCH.	FALSE
--max-diffs	INTEGER	Maximum number of different bases allowable in overlap.	5
--min-overlap	INTEGER	When merging, the minimum length of overlap between reads.	16
--maximum-expected-error	FLOAT	After merging, the allowable limit of erroneous bases.	1
--reference-chimera-filter	TEXT	Define a file path or set to true to use BLAST reference database.	TRUE
--minimum-sequence-abundance	INTEGER	When clustering, do not create any clusters with fewer than this many representative sequences.	2
--percent-of-allowable-difference	FLOAT	Maximum difference between an OTU member sequence and the representative sequence of that OTU.	3
--reference-database	[silva|greengenes|unite]	Two 16S databases are supported, SILVA and GreenGenes, along with Unite for ITS. References will be downloaded as needed during the execution of the workflow to the location set using --database-dir.	‘silva’
--blast-minimum-bitscore	INTEGER	Filter out alignments below this bitscore threshold and do not use them in the LCA calculation.	100
--blast-top-fraction	FLOAT	When calculating LCA, only use this fraction of HSPs from the best scoring alignment.	0.95
--read-identity-requirement	FLOAT	When mapping reads back to OTU seed sequences for quantification, require this fraction of sequence identity between sequence and reference.	0.97
--min-pid	FLOAT	Minimum percent ID required from VSEARCH hits in order to be retained for LCA calculation	0.85