Scythe on Helix
Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. It considers quality information, which can make it robust in picking out 3'-end adapters, which often include poor quality bases.
Most next generation sequencing reads have deteriorating quality towards the 3'-end. It's common for a quality-based trimmer to be employed before mapping, assemblies, and analysis to remove these poor quality bases. However, quality-based trimming could remove bases that are helpful in identifying (and removing) 3'-end adapter contaminants. Thus, it is recommended you run Scythebefore quality-based trimming, as part of a read quality control pipeline.
The Bayesian approach Scythe uses compares two likelihood models: the probability of seeing the matches in a sequence given contamination, and not given contamination. Given that the read is contaminated, the probability of seeing a certain number of matches and mistmatches is a function of the quality of the sequence. Given the read is not contaminated (and is thus assumed to be random sequence), the probability of seeing a certain number of matches and mismatches is chance. The posterior is calculated across both these likelihood models, and the class (contaminated or not contaminated) with the maximum posterior probability is the class selected.
The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands as in the example below.
$ module avail scythe -------------------- /usr/local/Modules/3.2.9/modulefiles ---------------------- scythe/0.981 $ module load scythe $ module list Currently Loaded Modulefiles:
1) scythe/0.981 $ module unload scythe $ module load scythe/0.981 $ module show scythe ------------------------------------------------------------------- /usr/local/Modules/3.2.9/modulefiles/scythe/0.981: module-whatis Sets up scythe 0.981 prepend-path PATH /usr/local/apps/scythe/0.981 -----------------------------------------------------------------
How To Use
$ scythe -a adapter_file.fasta -o trimmed_sequences.fasta sequences.fastq
