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**DECONSEQ**

Documentation by Sarah Shah, Shelby Williams

Source: [[http://deconseq.sourceforge.net/manual.html]] On perun: /opt/perun/deconseq-standalone-0.4.3 (copy this folder into your working directory)

Warning: If your read file is above 4GB, you must split it. Deconseq's Github page has also been abandoned since 2014, so do not expect an update or a fix for a bug.

This can be used to decontaminate reads using a database of your suspected contaminant sequences.

1. Make a bwa index by:

**bwa64 index -p prefix_of_your_choice_for_bacteria_index -a bwtsw fasta_file_of_your_suspected_bacteria >bwa.log 2>&1 &**

2. Move the 8 index files to the folder "db".

3. Edit the config file (DeconSeqConfig.pm) as such:

**bact => {name => 'Nameofyourchoice', db => 'prefix_of_bacteria_index'},**

Do not edit anything else.

4. Write a shell script (example below) and qsub it.

**#!/bin/sh**

**#$ -S /bin/sh**

**. /etc/profile**

**#$ -cwd**

**perl deconseq.pl -f Blasto_filtered.fastq -dbs bact -out_dir outfolder -keep_tmp_files -i 85  -id testdeconseq**

The "-f" is your read file, the "-i" is how identical your sequences must be to the bacteria to be thrown out, and the "-id" is a prefix of your choice that will be added to the names of your output read files.

5. Your shell script's error file should have a log of the number of sequences it is reading.

6. Your output folder should have: one "clean" reads file, one "contaminant" reads file, and a .tsv file of alignments between your read sequences and bacterial sequences.

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