### Helptext for TALEcorrection:#################################################
TALEcorrection is a java implemented tool that corrects TALE sequences in ONT sequenced Xanthomonas genomes. It contains three tools: 
1. The tool "prepare" is used to build custom TALE HMMs. 
2. The tool "correct" is doing the correction within TALE sequences based on the trained TALE HMMs. 
3. The tool "polish" is an optional polishing step to polish substitutions. This requires a mapping of the reads to the corrected assembly. 
To run these tools the folder TALEcorrection_scripts contains three different bash scripts explained in the following lines:

### First install:############################################################## 
# HMMER, see: http://hmmer.org/documentation.html					 
# clustalo, see: http://www.clustal.org/omega/ 					 
# igvtools, see https://software.broadinstitute.org/software/igv/igvtools_commandline 
################################################################################

### build custom TALE HMMs ###
1. If you want to build custom HMMs for TALEs of different strains, you can prepare and run bash script buildCustomHMMs.sh -> To prepare - please read comments within buildCustomHMMs.sh
# In case you want to correct TALEs in Xoo or Xoc genomes, you can use pre-built HMMs in folder HMMs/Xoo or HMMs/Xoc and you can skip step 1.

### run TALE correction ###
2. To correct TALE sequences within ONT assemblies, run the bash script runTALEcorrection.sh 
-> To prepare - please read comments within runTALEcorrection.sh to change settings to your purpose, like configuration of the matching pathovar.

### run substitution polishing ###
3. After runTALECorrection.sh, you can optionally run bash script runSubPolish.sh to polish inserted/substituted nucleotides based on mapping of reads to the corrected assembly
# Please map reads against the corrected assembly first
