DIAMOND-MEGAN

Diamond-Megan analysis: a practical case study

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0- Login and data accessibility

ls -lrth /media/D/util/DM/

1- Run Singularity

singularity

2- Run the image with Singularity

singularity shell /media/D/util/DM/DM.sif
exit

3- Check the test dataset

ls -lrth /media/D/util/DM/Test/

4- Create work folder and obtain the test dataset

mkdir Jclub
cd Jclub
cp /media/D/util/DM/Test/* .
ls -lrth

5- Map (or bind) the media drive and start with Fastq-Join

export SINGULARITY_BINDPATH="/media/D/"
singularity shell /media/D/util/DM/DM.sif
fastq-join BIO9-13J_S7_L001_R1_001.fastq.gz BIO9-13J_S7_L001_R2_001.fastq.gz -o join_Bio_%.fastq
ls -lrth

6- Merge the file and remove intermediates

cat *.fastq > BIO_merged.fq
rm *fastq
ls -lrth

7- Run Diamond with nr database or other subset DBs

time diamond blastx -q BIO_merged.fq -d /media/D/bank/nr/nr.dmnd -o D_nr_BIO.daa -f 100 -p 25
#Or other Diamond subset database (e.g. virus)  
time diamond blastx -q BIO_merged.fq -d /media/D/bank/Diamond/Vref-gb.dmnd -o BIO_RG.daa -f 100 -p 5  
exit

8- Link other DAA file to your folder

ln -s /media/D/util/DM/DAA/* .
ls -lrth

9- Run MEGAN and Start Meganization

MEGAN
/media/D/bank/nr/megan-map/megan-map-Feb2022.db

10- Optional: Meganization on command line

daa-meganizer -i FILE.daa -t 50 -mdb /media/D/bank/nr/megan-map/megan-map-Feb2022.db

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Naser Poursalavati, 2022