Kotori
bcbio-nextgen
| Kotori | bcbio-nextgen | |
|---|---|---|
| - | 2 | |
| 107 | 975 | |
| 1.9% | 0.2% | |
| 6.3 | 6.2 | |
| about 1 month ago | 10 days ago | |
| Python | Python | |
| Server Side Public License, v 1 | MIT License |
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Kotori
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Tracking mentions began in Dec 2020.
bcbio-nextgen
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Deep Sleep May Be the Best Defense Against Alzheimer’s
Re WGS there are a lot of well established tool chains that are FLOSS (eg https://github.com/bcbio/bcbio-nextgen). You could run alignment and variant calling on a beefy workstation. A laptop would potentially work. Easy to test this with publicly available raw data. Another option: The sequencing provider often will run alignment and some default variant calling for you. Annotating and analysing these variants can be done on pretty much any computer, all with open source software. A SNP chip is even easier to deal with as the computational requirements are less.
Interpreting the results is a more manual process. Really depends on what you are interested in.
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Advices on how to advance in the field to a beginner
There are plenty of workshops and free documentation online, a few from the top of my head : https://hbctraining.github.io/main/, https://software-carpentry.org/lessons/, https://github.com/bcbio/bcbio-nextgen.
What are some alternatives?
Pandas - Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more
SymPy - A computer algebra system written in pure Python
orange - 🍊 :bar_chart: :bulb: Orange: Interactive data analysis
MerkavaDB - A fast ordered NoSQL database.
Numba - NumPy aware dynamic Python compiler using LLVM
NumPy - The fundamental package for scientific computing with Python.
Dask - Parallel computing with task scheduling
Biopython - Official git repository for Biopython (originally converted from CVS)
NetworkX - Network Analysis in Python