SOP for ITS analysis using Sanger sequencing?

Kendra · January 3, 2019, 5:30pm

here’s an example of how to analyze sanger sequenced ITS, it’s several years old so some of the command defaults may have changed.
https://mothur.org/wiki/Forest_soil_community_analysis

you could also look at my batch file for miseq ITS, which is different data but should have current commands/options

github.com

krmaas/bioinformatics/blob/master/mothur.fungal.batch

###################################################################
###################################################################
###################################################################


##Basic mothur processing of MiSeq sequences using ITS2 primers.  This batch is based on mothur.org/wiki/MiSeq_SOP  All commands are explained in much more detail in that SOP. If your data is not demultiplexed, see the chunk of code at the bottom of this file.
##I use a computer with a high memory node (512gb RAM) with 32 processors. You'll need to adjust processors used to match your system. 


#############
##### I've started using basemount to download the fastq directly to the server. This will download and rename the files to include sample name and sample ID.
#p=PROJECTNAME
#mkdir -p $p/fastq
#for f in basespace/Projects/$p/Samples/*/Files/*.gz; 
#do s=${f##basespace/Projects/$p/Samples/}; s=${s%%/*}; 
#cp $f $p"/fastq/"$s"."${f##*Files/}; 
#done
#####################

### In addition to your sequence files and the oligos file, you need some files from the mothur website to be accessible (either in your path or in the folder you are working in). The line below moves them from my public directory on the BBC server to your current directory.

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SOP for ITS analysis using Sanger sequencing?

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