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meta.yaml
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meta.yaml
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name: nonpareil
description: Nonpareil uses the redundancy of the reads in metagenomic datasets to estimate the average coverage and predict the amount of sequences that will be required to achieve “nearly complete coverage”.
url: https://nonpareil.readthedocs.io/en/latest/
authors:
- Filipe G. Vieira
input:
- reads in FASTA/Q format (can be gziped or bziped)
output:
- redund_sum: redundancy summary TSV file with six columns, representing sequencing effort, summary of the distribution of redundancy (average redundancy, standard deviation, quartile 1, median, and quartile 3).
- redund_val: redundancy values TSV file with three columns (similar to redundancy summary, but provides ALL results), representing sequencing effort, ID of the replicate and estimated redundancy value.
- mate_distr: mate distribution file, with the number of reads in the dataset matching a query read.
- log: log of internal Nonpareil processing.
params:
- alg: nonpareil algorithm, either `kmer` or `alignment` (mandatory).
- extra: additional program arguments