SURPI v1.0.18

• removed bug (in extractHeaderFromFastq_ncores.sh) and synchronized code with AWS AMI

SURPI v1.0.17

• Added documentation
• Added SURPI installer
• Added scripts to create all necessary reference databases
• Updated license to BSD 2 clause
• Removed many extraneous command line options - now config file is required for SURPI runs
• separated SNAP edit distance for human subtraction and NT alignment into separate config file parameters
• Added check after preprocessing step to stop pipeline if null FASTQ file
• bugfixes
• Added additional software dependency (GNU parallel), which is used to parallelize and throttle some SURPI processes
• Updated SURPI_installer.sh to install the correct SURPI version (1.0.17)

SURPI v1.0.13

• Added ribosomal cleanup
• Cleaned up logfiles
• Bugfixes
• SURPI v1.0.13 is the version used on the updated Amazon EC2 AMI also released today.

SURPI v1.0.11

• Added error checking to SURPI to help determine if a failure is due to a software dependency or a reference data issue

SURPI will now check all software dependencies and reference data at the beginning of the pipeline. Check the log file for information on this verification. In short, each check will either show "OK" (in green, if your terminal supports color), or "BAD" (in red).

SURPI v1.0.10

bugfixes

SURPI v1.0.9

• added command line option (-v) for verification mode. In this mode, SURPI will verify all dependencies, reference data, and FASTQ file (if desired). The actual pipeline is not run - only verification occurs.

This same verification is also done at the beginning of every pipeline run. Results are within the log file generated by the pipeline.

• adjusted SNAP - nt to remove intermediate .sam files upon completion. These files were not deleted by the recently added compare_multiple_sam.py method.

SURPI v1.0.8

Added checks to the beginning of SURPI:

• verify software dependencies are installed properly
• verify reference data is available
• verify taxonomy is functioning (already added in a past release)

Cleaned up some config file parameters

• removed extraneous RAPSearch folder & included this information in the RAPSearch databases
• Adjusted SNAP folder names

SURPI v1.0.7

SNAP-nt

Added option to do comparison at end of all SNAP portions rather than after each individual. This will allow for further upcoming optimizations.

• Cleaned some echo commands within several scripts
• Updated readme

SURPI v1.0.6

• moved several parameters to config file

taxonomy database directory

temporary files directory

SURPI v1.0.5

Includes latest version of taxonomy lookup, which is significantly faster than previous versions.