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- Hard trims FASTQ, if optionally specified (fastx_trimmer)
- Performs the global or local alignment (here, a PE alignment)
- BWA global: bwa aln the R1 and R2 separately, then bwa sampe to produce a SAM file
- BWA local: call bwa mem with both R1 and R2 to produce a SAM file
- Bowtie2 global: call bowtie2 in its default global (end--global with to-end) mode on both R1 and R2 to produce a SAM file
- Bowtie2 local: call bowtie2 --local with both R1 and R2 to produce a SAM file
- BWA global: bwa aln the R1 and R2 separately, then bwa sampe to produce a SAM file
- Converts SAM to BAM (samtools view)
- Sorts the BAM (samtools sort)
- Marks duplicates (Picard MarkDuplicates)
- Indexes the sorted, duplicate-marked BAM (samtools index)
- Gathers statistics (samtools idxstats, samtools flagstat, plus a custom statistics script of Anna's)
- Removes intermediate files
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