Role to clean up orphan reads in a fastq file
Dont do --discard for error correction and make ropebwt default indexing algorithm
Add ability to accept one shuffled fastq file for preprocessing
Merge branch 'master' into add_sga_step
Revert "Add ability to accept one shuffled fastq file for preprocessing"

This reverts commit 77116c14a5a7cfe39075ca1f3a7a8be9095b0487.
Make -d default value 1000000
Make default indexing algorithm ropebwt
Make -d default 1000000 and algorithm ropebwt
Merge pull request #19 from nds/add_sga_step

Add sga step