Profile long reads

Since mOTUs 3.0.3 it is possible to profile long reads with mOTUs.

Given a long read fasta file (let's say long_reads.fasta), you need to first run:

motus prep_long -i long_reads.fasta -o converted_long_reads.fasta.gz

to split the long reads into shorter reads that can be profiled by a default mOTUs profile call like:

motus profile -s converted_long_reads.fasta.gz

Note that the command prep_long works on both fasta and fastq files, as well as on .gz files.

How to install mOTUs

mOTUs 3.0.3 is still not avaialable on bioconda (we are working on it!), but you can download it from pip:

pip install motu-profiler

Note that you have to install the following dependencies manually:

• python >=3.6.5
• bwa >=0.7.17
• SAMtools >=1.6

For example using conda directly, or creating an environment through conda, like:

conda create -n motus303 python>=3.6.5 pip bwa>=0.7.17 samtools>=1.6