Masking Low Complexity Regions – Step-by-Step

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Bioinformatics

This short tutorial teaches how to mask low complexity regions in a FASTA file. This can be quickly accomplished by using bbmap which can download using bioconda.

How to Mask Low Complexity Regions in a FASTA File

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

This can be easily done using bioconda as we show below:

$ conda install -c bioconda bbmap

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

$ bbmask.sh in=INPUT out=MASKED_OUTPUT entropy=0.7

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