Simple examples
The mOTUs profiler is a computational tool that estimates relative abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data. The profiling method is based on ~100,000 universal single-copy marker genes that have been extracted from more than 3,000 metagenomic samples and ~25,000 reference genomes.
The taxonomy profiling shown here can be executed with:
motus profile -f sample1.for.fastq -r sample1.rev.fastq -n sample1 -o s1.motu
motus profile -f sample2.for.fastq -r sample2.rev.fastq -s sample2.single.fastq -n sample2 -o s2.motu
motus merge -i s1.motu,s2.motu -o all_samples.motu
The SNV calling shown on the right can be executed with:
mkdir bam_files
motus map_snv -f sample1.for.fastq -r sample1.rev.fastq -o bam_files/s1.bam
motus map_snv -f sample2.for.fastq -r sample2.rev.fastq -s sample2.single.fastq -o bam_files/s2.bam
motus snv_call -d bam_files -o SNV_profiles