lecture_notes:04-20-2015
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision | ||
|
lecture_notes:04-20-2015 [2015/04/25 03:03] calef [User experience] |
lecture_notes:04-20-2015 [2015/04/25 03:07] (current) calef [Error correction] |
||
|---|---|---|---|
| Line 22: | Line 22: | ||
| * Requires an array of other scripts in other languages | * Requires an array of other scripts in other languages | ||
| * Most of high level scripts are written in perl | * Most of high level scripts are written in perl | ||
| - | * Runs from a shell script and a user-provided config file | ||
| - | * SGE-aware, handles qsub and monitoring jobs | ||
| - | * Pipeline is well sub-divided, running the program produces intermediate files and executables allowing the user to suspend, resume, or restart the run from any step in the pipeline | ||
| - | * Thorough error logging for each step in the algorithm | ||
| * Tested the program with the packaged test data and obtained contigs | * Tested the program with the packaged test data and obtained contigs | ||
| =====Installation===== | =====Installation===== | ||
| Line 33: | Line 29: | ||
| * Some scripts contain error but they aren't hard to fix. | * Some scripts contain error but they aren't hard to fix. | ||
| =====Running Meraculous===== | =====Running Meraculous===== | ||
| - | * Execute run_meraculous.sh scripts along with the configuration file | + | * Execute run_meraculous.sh scripts along with user-provided configuration file |
| * Configuration file contains info on where where data is and what format it comes in | * Configuration file contains info on where where data is and what format it comes in | ||
| - | * It creates a timestamped folder that includes directories containing results of each step and executables to modify the run | + | * Creates a timestamped folder that includes directories containing results of each step and executables to suspend, resume, or restart the run from that step |
| - | * Then you can check the errors that made a run fail and resume the run | + | * Thorough error-logging at each step, allowing you to check the errors that made a run fail and then resume the run after fixing the errors |
| - | * Logs are informative | + | * SGE-aware, handles qsub and monitoring jobs |
| =====Overall impression===== | =====Overall impression===== | ||
| * Straightforward to figure out what went wrong just requiring a basic understanding of Perl | * Straightforward to figure out what went wrong just requiring a basic understanding of Perl | ||
| Line 43: | Line 39: | ||
| * Logs are very useful | * Logs are very useful | ||
| =====Error correction===== | =====Error correction===== | ||
| - | * Meraculous requires error correction and adapter removal. Trimming is unnecessary. | + | * Meraculous requires error correction and adapter removal. Trimming is unnecessary, as low quality reads are ignored during contig formation. |
| - | * High error rates stop the assembler. Need to be removed. | + | * High error rates bog down the assembler. Need to be removed. |
| * Kmer size chosen directly affects assembly quality | * Kmer size chosen directly affects assembly quality | ||
| =====KamerGenie===== | =====KamerGenie===== | ||
lecture_notes/04-20-2015.1429931022.txt.gz · Last modified: 2015/04/25 03:03 by calef
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial-Share Alike 3.0 Unported
