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
More Resources
- Fast Conversion of Lowercase Sequences to Uppercase in FASTA Format
- Easy NCBI Genome Download
- The Fastest Way to Read a FASTA in Python
