Recently, while helping my senior sister with sequence alignment, I discovered that the software I used to use frequently, MEGA X (10), now has a Linux GUI version. This made me feel that the world is indeed changing.

I recently discovered GNU Parallel, a simple and useful parallel program implemented in Perl, which can easily execute various commands in Bash in parallel. This is particularly useful for tasks that can be divided into independent subtasks.

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.

“I know a lot about structural variation information,” but the content of this blog post is too much, and it’s not convenient for me to look back. So I decided to split it into smaller parts and write a comprehensive one using GitBook later.

I didn’t expect to do regression again after four years… this time using R instead of SPSS. Previously, I was doing statistical analysis, but now… it’s machine learning.

After using snakemake for some time, I found that it has many practical features to facilitate daily analysis. Here is a record and整理.

I’ve never used many useful functions when writing scripts before, so I decided to learn a bit about itertools and make some notes. This time, I was dealing with large files, but most of the time, ...

R provides convenient multiprocessing capabilities, and Python has similar functionality.

Recently, I wrote a script to draw many images using ggplot. Although all the places where loops are needed have already been replaced with apply, it still can’t keep up when drawing hundreds of images at once. So, I fiddled around with parallel and managed to parallelize the plotting part to speed things up.

It’s been a while since the last update. Today, I’ll record the upgraded version of my homemade VPN!