yomama

yomama is a console-based application for preparing and processing sequencing data from multiplexed amplicon datasets.  
These datasets contain seqeuncing from multiple amplicons across many individual samples barcoded into a run of MiSeq, PGM, or other instrument. 
This type of data can be produced by Fluidigm Access Array, Ampliseq, Trueseq amplicon seqeuncing, or any other technology that generates amplicon data.

Preparing includes reading fastq or fasta/qual files, debarcoding, delinkering, deprimering and quality filtering.

Processing includes calling SNPs, aligning and doing microsatellite or heteroplasmy analysis.

A typical session involves the user setting configuration options, reading and preparing input files, and performing one of the above-mentioned "processing" steps. Interactive output is available on the screen, and output files can be written in standard formats (fasta, vcf, etc.).

Configuration options and prepared reads persist between sessions. A saved command history and the ability to run scripts are desired additions.