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Update docs/output.md

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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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Sofia Stamouli 2023-01-11 16:47:18 +01:00 committed by GitHub
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@ -235,7 +235,7 @@ You will only recieve the FASTQs and `*classifiedreads.txt` file if you supply `
<summary>Output files</summary> <summary>Output files</summary>
- `krakenuniq/` - `krakenuniq/`
- <db_name>/ - `<db_name>/`
- `<sample_id>_<db_name>.classified.fastq.gz`: FASTQ file containing all reads that had a hit against a reference in the database for a given sample - `<sample_id>_<db_name>.classified.fastq.gz`: FASTQ file containing all reads that had a hit against a reference in the database for a given sample
- `<sample_id>_<db_name>.unclassified.fastq.gz`: FASTQ file containing all reads that did not have a hit in the database for a given sample - `<sample_id>_<db_name>.unclassified.fastq.gz`: FASTQ file containing all reads that did not have a hit in the database for a given sample
- `<sample_id>_<db_name>.report.txt`: A Kraken2-style report that summarises the fraction abundance, taxonomic ID, number of Kmers, taxonomic path of all the hits, with an additional column for k-mer coverage, that allows for more accurate distinguishing between false-positive/true-postitive hits - `<sample_id>_<db_name>.report.txt`: A Kraken2-style report that summarises the fraction abundance, taxonomic ID, number of Kmers, taxonomic path of all the hits, with an additional column for k-mer coverage, that allows for more accurate distinguishing between false-positive/true-postitive hits