sorts sequenced reads into separate files for each sample in a sequenced run
Trimming reads
-create Bash script to iterate through basenames (lacking R1 or R2) and execute NGmergeNGmerge -1 sample_R1.fastq.gz -2 sample_R2.fastq.gz -o sample_merged.fastq.gz
MPI-based parallelized BWA mem alignment to the W303 genome (fastq->SAM)
-Output is a tab-delimited text file w/ information for each individual read and its alignment to the genome
gatk MarkDuplicatesSpark to mark duplicates and sort
-MarkDuplicatesSpark utilizes Apache Spark in order to parallelize the process to better take advantage all available resources
samtools view (SAM->BAM)
-Output is a compressed binary version of SAM. This version reduces size and to allows for indexing, which enables efficient random access of the data contained within the file.