Actually, I’ve known about singularity for quite some time. As a container specifically designed for HPC (High Performance Computing), it’s always been something I wanted to try out. However, just like other NGS technologies outside of Illumina, singularity hasn’t gained much traction and it seems even harder to compete with Kubernetes, which is widely adopted by most cloud vendors… Of course, this doesn’t really matter to me right now… We’re still at least three or five years away from going cloud-based, so using it locally makes perfect sense.

mSINGS is a software tool used to detect MSI (Microsatellite Instability). Its advantage seems to be that it can be used for tumor-only samples.

MultiQC is a tool for NGS data quality control. Unlike many other tools, it does not directly obtain and calculate metrics; instead, it reads results files from various common quality control tools and provides comprehensive reporting.

Lumpy’s author positioned this project more as building a general structural variant signal generation scheme rather than creating an excellent tool. It was implemented as a basic version of the scheme. Compared to other tools, Lumpy spent more time in its article explaining the evidence concepts and methods for obtaining information. Interpreting this tool has made me understand better how to obtain structural variant signals from NGS sequencing data.

Writing workflows is a common task in bioinformatics analysis, and a mature and well-designed tool can greatly improve the efficiency of work.

When using SGE at a new company, the approach is somewhat different. Here are some notes.