elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard, and was extensively tested with the GATK best practices pipeline for variant analysis.
elPrep-mongo is an extension of elPrep that allows for using MongoDB databases as input and/or output targets in elPrep, on top of the in-memory and file representations that elPrep already supports.
For more details on elPrep, please visit the elPrep github repository.
A rudimentary example for the use of elPrep-mongo is provided in example.lisp. Please use the input data from the elPrep demo with this example.
A specification for the representation of SAM files in MongoDB databases is also provided as part of this repository.
The elPrep-mongo implementation depends on elPrep and cl-mongo-stream, which have further dependencies that you may need to check. The elPrep-mongo implementation also depends on the string-case library which is available through the quicklisp package manager.