Tools

Lotus pipeline

LotuS offers a lightweight complete 16S/18S/ITS pipeline to

• Demultiplex and filter fasta or fastq sequences
• Denoise, remove chimeric sequences and cluster sequences into very high quality OTUs that perform at a similar level to mothur / dada2
• Determine taxonomic origin of each OTU using >5 spezialized and general purpose database or statistical algorithms
• Construct OTU, genus, family, class, order and phylum abundance tables in .txt or .biom format
• Reconstruct OTU phylogenetic tree

More information at LotuS home page

usearch

Download usearch version 8 and copy the executable in a folder e.g. /usr.bin/tools/ which you can reach (you might to be superuser for this)

Make executable:

sudo chmod +x /usr/bin/tools/usearch8.1.1861_i86linux32

Create a symbolic link into the folder where Lotus will search for it:

sudo ln -s /usr/bin/tools/usearch8.1.1861_i86linux32 /usr/bin/tools/lotus_pipeline/bin/usearch_bin `

R package

You also need R with the vegan package installed.

keypoints Key points

• We presented the tools for the training and the data files

Useful literature

Further information, including links to documentation and original publications, regarding the tools, analysis techniques and the interpretation of results described in this tutorial can be found here.