How to run YAMP with QC'ed reads

This tutorial aims at explaining how to run YAMP using reads that have externally QC'ed.

Format your input file

To use YAMP with externally QC'ed sequences you need to create a file structure that is compatible with the one created by YAMP. To do so, you should:

1. create a folder called outputdir/mysample where outputdir is the directory where the results will be stored and mysample is a prefix that will be used to label all the resulting files (as explained in the How to run YAMP tutorial). These two parameters will be used also to run YAMP.
2. (if needed,) collapse the QC'ed files in a single FASTQ file that should be saved in the outputdir/mysample as mysample_clean.fq. If you have paired-end QC'ed reads you can use the following command:

	bbmerge.sh in1=read1.fq in2=read2.fq out=mysample_clean.fq

Please note that the file should not be compressed (that is is should be mysample_clean.fq and not mysample_clean.fq.gz).

Run YAMP

We can now run YAMP with the following command:

	nextflow run YAMP.nf --prefix mysample --outdir outputdir --mode characterisation

where mysample and outputdir are those used in the step above