Helpful_scripts_and_things

Scripts I write (or sometimes partially steal but try to give credit) that help me get through some issues with various software (usually just formatting) and some tips for novices running bioinformatics software packages.

1. Quick reformat of MAUVE XMFA file for ClonalOrigin
2. Thoughts about slow running warg jobs
3. Tips for running Trinity outside a VM
4. Doing some simple column formatting gymnastics to help reformat .map and .ped files (and others) for GWAS with PLINK
5. Merging Illumina sequencer run data after multiple runs to give output data with the same name
6. Old Perl script converting raw 3730 seq files to fasta files
7. Some oneliners Like
   • Removing the >ref| from the header lines of NCBI downloaded genome files
   • Changing file extensions recursively
   • Proper or improved use of grep with big files on an HPC