Commit f62a6ce7 authored by Overduin, Sam's avatar Overduin, Sam
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Update README.md

parent d42eeabb
......@@ -10,7 +10,7 @@ For more information please contact the author, Sam Overduin.
# Overview
The pipeline consists of 3 steps that should be run manually: read taxonomy assignment with Kraken2, read annotation with scripts/append_taxatree_to_reads.py and taxaSPAdes.
## Kraken2
## 1. Kraken2
1. Read taxonomy assignment with Kraken2.
This step requires Kraken2 to be installed already with a database. If this is not the case, download Kraken2 from [here](https://ccb.jhu.edu/software/kraken2/index.shtml?t=downloads), install and set up the database according to the instructions [here](https://ccb.jhu.edu/software/kraken2/index.shtml?t=manual).
......@@ -23,7 +23,7 @@ Using ```--confidence 0.2``` is important for the quality of taxonomic assignmen
It is possible to use a different tool than Kraken2 to taxonomically annotate the reads. In this case be sure to check what columns of the output file contain the read header and taxonomy ID.
## Read annotation
## 2. Read annotation
2. Read annotation with scripts/append_taxatree_to_reads.py
This step adds taxonomic annotation to the reads in the form of TaxaTree:1.2.3.4.
......@@ -55,7 +55,7 @@ Defines 0-based index of column containing taxID in kraken_file. Useful if using
```--read_pos or -rp```
Defines 0-based index of column containing read header in kraken_file. Useful if using a different tool than Kraken2. Default=1.
## TaxaSPAdes
## 3. TaxaSPAdes
3. Run taxaSPAdes with the annotated reads
Run taxaSPAdes with the following parameters:
```bash
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