- the simple single thread bowtie job
- the multi-thread job taking advantage of bowtie2's parallel support for better performance. It is recommended to use bowtie2 this way when dealing with large alignment job, such as build hg38 human genome index. Please note, the E.Coli reference is used in the example, for demo purpose.
a. Bowtie 2 indexes work only with v2 (not v1). Likewise for v1 indexes. If the wrong version of index is used when using bowtie2 aligner, it could be the cause of many weird memory segmentation errors observe.
b. some commonly used reference indexes are already built on SCC, they are under $SCC_BOWTIE2_REF directory. Please take a look at it and maybe it could save you some time to build the reference indexes by yourself.