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 |