Chapter 12 ATLAS-Pipeline

ATLAS-Pipeline will easily convert all of your fastq-files into bamfiles in parallel, perform local realignment, recalibrate your base quality scores and correct your data for Post-Mortem Damage by combining the most standard tools into one pipeline while keeping high flexibility. Further, you can directly call variants, create vcf/glf files or estimate the heterozygosity of your samples.

The complete ATLAS-Pipeline is split in four modules. Each module can be invoked separately and independently:

• Gaia - Genome Wide Alignment including Adapter-trimming.

• Rhea - Local InDel-Realignment.

• Perses - Post-Mortem-Damage and Error Rate Estimation for Sequence Data.

• Pallas - Population ALLele-frequency AnalysiS.