* Changed bowtie2 settings from --very-sensitive to --very-sensitive-local * Checking 1st and last 100 seq and removing spaces from seq identifiers if present * Add min len to start of trimmomatic run to try to resolve trimmomatic hanging during adapter trimming with short reads
0.8.0
* Add another bowtie2 option for filtering of paired end reads. This "strict" mode, the new default, removes both reads if either pair aligns. Modify existing pair alignment options into a single option.
0.7.10
* Remove trim-repetitive sequences option (prior set as default for filtering to remove adapters and overrepresented sequences). * Add more adapters plus option to select adapter type.
0.7.9
* Modified check for ordered pairs to only check the first 100 sequence ids to reduce memory usage. * Move resolve sublists to allow for multiple lists in final output files (resolves error with running with multiple databases).
0.7.8
* Remove temp files from decompression and reformatting after they are no longer needed to save space. * Update SILVA_128_LSUParc_SSUParc_ribosomal_RNA to Version 0.2 * Change to the read mode for the decompress function for bz2 files for python 3 compatibility.
0.7.7alpha
* Changes in the workflow order of TRF and bowtie2 * Add trim-repetitive option flag to remove adapters and overrepresented sequences.