aDNApipeline

Usage:

Single ended

adnapipe_single.bat fastq threads Population name Individual name

OR

pipeline_single.bat fastq threads Population name Individual name

Example: adnapipe_single.bat ERR2744350.fastq.gz 8 Israel I1165

Paired

adnapipe_paired.bat fastq_1 fastq_2 threads Population name Individual name

OR

pipeline_paired.bat fastq_1 fastq_2 threads Population name Individual name

Example: adnapipe_paired.bat ERR4300339_1.fastq.gz ERR4300339_2.fastq.gz 8 German kra005

The program downloads hs37d5.fa if it does not exist in the main directory. The program will also create bwa index of hs37d5.fa if it is missing.

Notice! Do not use spaces in any arguments!