SECRAM

SECRAM is a library for compressing, encrypting, and querying alignment data. The library is designed to achieve three important features: high security/privacy, low storage cost, fast random access. SECRAM v1.0 consists of the following:

• A converter from BAM file to SECRAM file
• A converter from SECRAM file to BAM file
• A basic query API for random access of SECRAM file

System requirement

This library is tested on:

• Java version 1.8.0_45
• Mac OS X Yosemite version 10.10.5

Basic usage

Some example uses of the library are in the package com.sg.secram.example (both the src and test folder.). There are also several basic functionalities provided in the class com.sg.secram.Main. Run the Main class with argument:

• --help: Show the help menu.
• keygen -o my.key: Generate a master key for the encryption/decryption.
• bam2secram -k my.key -r my_reference.fa -i my_bam_file.bam -o my_secram_file.secram: Convert the BAM file (my_bam_file.bam) to the SECRAM file (my_secram_file.secram) by using the reference file (my_reference.fa) and the master key (my.key).
• secram2bam -k my.key -r my_reference.fa -i my_secram_file.secram -o my_bam_file.bam: Convert the SECRAM file (my_secram_file.secram) to the BAM file (my_bam_file.bam) by using the reference file (my_reference.fa) and the master key (my.key).

Requirement when running with reference genome GRCh37

To successfully run the code with reference genome GRCh37, please follow the steps below.

Download the human reference genome in the link:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz

Decompress the file:

gunzip hs37d5.fa.gz

Create an index file:

samtools faidx hs37d5.fa

Put the two files hs37d5.fa and hs37d5.fa.fai in the folder data/.

Releases

• Version 1.0

Contact

Zhicong Huang (zhicong.huang@epfl.ch)