16SMaRT
covid-19-signal
16SMaRT | covid-19-signal | |
---|---|---|
3 | 1 | |
7 | 30 | |
- | - | |
0.0 | 5.2 | |
over 1 year ago | 9 days ago | |
Python | Python | |
MIT License | MIT License |
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16SMaRT
covid-19-signal
-
What does a typical whole genome sequencing of SARS-CoV-2 fastq file look like?
For an example pipeline, check out SIGNAL - there is a workflow diagram in that repo https://github.com/jaleezyy/covid-19-signal
What are some alternatives?
ariba - Antimicrobial Resistance Identification By Assembly
drep - Rapid comparison and dereplication of genomes
hgvs - Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
metaflow - :rocket: Build and manage real-life ML, AI, and data science projects with ease!
easy-entrez - Retrieve PubMed articles, text-mining annotations, or molecular data from >35 Entrez databases via easy to use Python package - built on top of Entrez E-utilities API.
Sacred - Sacred is a tool to help you configure, organize, log and reproduce experiments developed at IDSIA.
galaxy - Data intensive science for everyone.