Takes any fasta file for a reference, builds the index and then maps reads to the index. The index is saved in tar.gz form. Colorspace mapping is not available in this version, but this version maps much longer read sequences.
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> bowtie.
Use e_coli_1000_1.fq from the directory above as test input, and e_coli.fa as the reference.
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
Use ecoli as the prefix name and leave the input file format as fastq. The output file name can be left as the default BowtieOut.sam.
Expect a text file named after the input files as output. For the test case, the output file you will find in the example_data directory is named BowtieOut.sam.
The output .sam file should look similar to the e_coli_1000_pe.sam file in the example_data directory, which is the result if paired end sequencing is tested with e_coli_1000_1.fq and e_coli_1000_2.fq.
Discover Variants Using SAM Tools (Workflow Tutorial)