Masking Low Complexity Regions – Step-by-Step



This tutorial teaches how to mask low complexity regions in a FASTA file using BBMap.

1. How to Mask Low Complexity Regions in a FASTA File

First, we need to install BBMap, which comes with to mask low complexity regions.

I would recommend using Bioconda to install it using the command below:

$ conda install -c bioconda bbmap

Now that we have bbmask, we can use it to mask a FASTA file using an entropy of 0.7

$ in=INPUT out=MASKED_OUTPUT entropy=0.7

2. More Resources