From 2e08c873a0f0cc6011a134a7f34c28f6bf4c7e03 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Date: Tue, 20 Dec 2022 17:34:19 +0100 Subject: [PATCH] Apply review suggestion Co-authored-by: James A. Fellows Yates --- docs/output.md | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/docs/output.md b/docs/output.md index 7249c62..1a3ce7d 100644 --- a/docs/output.md +++ b/docs/output.md @@ -187,6 +187,24 @@ Note that the FASTQ file(s) may _not_ always be the 'final' reads that go into t +### Bracken + +[Bracken](https://ccb.jhu.edu/software/bracken/) (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Braken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. + +> 🛈 The first step of using Bracken requires running Kraken2, therefore the initial results before abundance estimation will be found in `/kraken2/`. + +
+Output files + +- `kraken2/` + - `bracken__combined_reports.txt`: combined bracken results as output from Bracken's `combine_bracken_outputs.py` script + - `/` + - `_.tsv: TSV file containing per-sample summary of Bracken results with abundance information + +
+ +The main taxonomic profiling file from KrakenUniq is the `*.tsv` file. This provides the basic results from Kraken2 but with the corrected abundance information. + ### Kraken2 [Kraken](https://ccb.jhu.edu/software/kraken2/) is a taxonomic sequence classifier that assigns taxonomic labels to DNA sequences. Kraken examines the k-mers within a query sequence and uses the information within those k-mers to query a database. That database maps -mers to the lowest common ancestor (LCA) of all genomes known to contain a given k-mer.