The bwa-mem story.
Hi bwa users,
The bwa-mem manuscript has been rejected. Interestingly, the first reviewer only raised a couple of minor concerns and then accepted the manuscript in the second round of the review. The second reviewer made quite a few mistakes on some basic concepts and was hostile from the
| # | |
| # What are the mapping percentages for the ebola data in | |
| # the Zaire ebolavirus sample sequencing from the 2014 outbreak | |
| # in Sierra Leone, West Africa | |
| # | |
| # http://www.ncbi.nlm.nih.gov/bioproject/PRJNA257197/ | |
| # Get the run info that corresponds to this project. | |
| # Get all the runs for this project. |
| #!/bin/bash | |
| # | |
| # Cue the music: https://www.youtube.com/watch?v=JtyByefOvgQ | |
| # | |
| # | |
| # Edit (Sept 2015): due to an unreasonable slowness of ncbi the script now requires | |
| # that you fetch the runinfo fetch once before starting the script | |
| # It should not really be slow but it takes almost 30 secons. | |
| # |
| # | |
| # FastQC style de-duplication stats and plot | |
| # | |
| # | |
| # The input file for this program needs to be generated via the command line with | |
| # a command like so: | |
| # | |
| # cat data.fq | bioawk -c fastx '{ print substr($seq,1, 50) } ' | sort | uniq -c | sort -k1,1 -rn > data.uniq.txt | |
| # | |
| # see bioawk at: https://github.com/lh3/bioawk |