Useful productivity tools for bioinformaticians
6
0
Entering edit mode
4.5 years ago
Pappu ★ 2.1k

I am wondering which productivity tools you use as a bioinformatician to improve the productivity of day to day work. For example using git, nextflow etc.

RNA-Seq ChIP-Seq R next-gen Python • 1.8k views
ADD COMMENT
5
Entering edit mode

You mean aside from the coffee-maker?

ADD REPLY
4
Entering edit mode

I label my bioinformatics calendar as "before Snakemake" and "after Snakemake"

ADD REPLY
1
Entering edit mode

"Other workflow managers are available".

But yeah. Use a workflow manager

ADD REPLY
1
Entering edit mode

I would highly recommend this book "wicked cool shell scripts" https://nostarch.com/wicked2 . One of my favorites from the book is the command line notepad . Most times you are on the terminal and want to write a quick note without moving, it can be easily done with the note shell script. note . The notes are saved to the file .Remember in the home. I twicked it by adding git and date and timestamps to notes. The book is littered with Gems.

ADD REPLY
3
Entering edit mode
4.5 years ago
GenoMax 143k

Basic unix commands cut/paste/sort/uniq/sed. Never designed for bioinformatics but very useful nonetheless.

For those that use windows as desktop OS notepad++ and MobaXterm.

ADD COMMENT
3
Entering edit mode
4.5 years ago
Joe 21k

I second ncdu.

I also like:

I have a lot of sysadminy stuff rather than pure productivity per se. Lots of my productivity is just stuff in dotfiles.

Undoubtedly loads more I forget now.

ADD COMMENT
2
Entering edit mode
4.5 years ago

an obvious one: awk ! :)

ADD COMMENT
2
Entering edit mode
4.5 years ago

ncdu for checking disk space used and number of files: https://linux.die.net/man/1/ncdu

ADD COMMENT
1
Entering edit mode
4.5 years ago
gb ★ 2.2k

https://atom.io/packages/split-diff And then using it for "normal" non code text files

ADD COMMENT
0
Entering edit mode
2.3 years ago

Asana, Trello are good ones

ADD COMMENT

Login before adding your answer.

Traffic: 2464 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6