README.Rmd

---
title: "DiaMet"
output: 
  md_document:
    variant: gfm
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  message = FALSE,
  warning = FALSE,
  comment = "#>"
)
```

# DiaMet
This repository aims to analyze those metagenomic Illumina reads that were unable to
be classified by [VirMet](https://github.com/medvir/VirMet) (`undetermined_reads.fastq.gz`)
by aligning them on protein level using [DIAMOND](https://github.com/bbuchfink/diamond)/BLASTx.

`diamet.py` analyzes all reads from `undetermined_reads.fastq.gz`

- as single reads, and

- as contigs created by *de novo* assembly using [megahit](https://github.com/voutcn/megahit).

### How to run

1. Enter timavo.

`ssh timavo`

2. Move into the directory of the sample whose undetermined reads you want to analyze.

`cd /analysis/VirMet/<run>/<sample>/`

3. Run the python script.

`python <path to script>/diamet.py`

### Input

To run `diamet.py`, you need:

- the `diamond` unix executable file which can be found [here](https://github.com/bbuchfink/diamond);

- [megahit](https://github.com/voutcn/megahit) installed on the server;

- a protein database (defined in the code; we are using *swissprot*);

- `undetermined_reads.fastq.gz`, which should be in the current working directory.

### Output

`diamet.py` will output the following files:

- `undetermined_reads_diamet.pdf` which plots taxonomic classification distribution of all hits;

- `undetermined_reads_diamet.tsv` which lists all hits and their Query Seq - id (qseqid),
Query sequence length (qlen), Alignment length (length), Unique Subject Scientific Name (sscinames),
and Unique Subject Super Kingdom (sskingdoms);

- `undetermined_reads_diamet_viral.csv` which lists only the viral hits and their counts;

- `undetermined_contigs_diamet.tsv` which lists all hits of the contigs and their 
Query Seq - id (qseqid), Query sequence length (qlen),Alignment length (length), 
Unique Subject Scientific Name (sscinames), and Unique Subject Super Kingdom (sskingdoms).