Tools used with UMI-Reducer

Samtools

Samtools is used to index the bam file before duplicates can be removed using collapsePCRduplicates.py

How to install:

First, visit https://github.com/samtools/samtools/releases/ to find the latest release. Under the downloads section right click on samtools-1.X.tar.bz2 and select Copy Link Address. On the command line enter:

wget (paste the link address)

When the file finishes downloading unzip it using

bunzip2 samtools-1.X.tar.bz2

and extract the file with:

tar -xvf samtools-1.X.tar

This will create a new directory called samtools-1.X. Change to this directory and enter

./configure

Pysam

Pysam is used in python to read the bam file that is input into UMI-Reducer.

How to install:

Visit the Github for Pysam, https://github.com/pysam-developers/pysam. In the top right corner click on the green button that says "Clone or download." Copy the web URL that appears under that button then go back to the command line and enter the following:

git clone (paste URL)

Feh

Feh is an image visualizing tool that is used to view the .png files output by UMI-Reducer

How to install: