Pipeline For Amplicons Analysis

Question

[konstantinkul]

Hi all! Could you recommend any pipelines for analysis of amplicons ? Is supposed that we will analyze the data from MiSeq (PE reads 2 x 150bp, file format fasta or fastq). I'll be thankful for any information.

Answer 1

[Sean Davis]

Take a look at GATK from the Broad and Picard library for quality control.

[konstantinkul]

Thanks a lot I'll try !