gatk4-genome-processing-pipeline-azure
seqkit
| gatk4-genome-processing-pipeline-azure | seqkit | |
|---|---|---|
| 4 | 3 | |
| 7 | 1,208 | |
| - | - | |
| 0.0 | 8.5 | |
| 2 months ago | 16 days ago | |
| wdl | Go | |
| BSD 3-clause "New" or "Revised" License | MIT License |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
gatk4-genome-processing-pipeline-azure
- What are some good examples of well-engineered bioinformatics pipelines?
-
Do you know how to get CNVs out of WES data sorted.bam files? (Free)
The GATK suite is pretty standard for calling germline mutations. Somatic mutation calling is a lot newer/trickier, so I'm just going to link to the GDC's practices.
-
Best way to document tool?
This pre-processing pipeline from Microsoft (adapted from the Broad Institute/GATK) is pretty well-documented - at least in my opinion - with input requirements, expected outputs, software requirements, etc.
seqkit
-
A look at the Mojo language for bioinformatics
I've been thinking to learn Rust for these use cases, but always get frustrated with the complexity.
I find Go is a great middle-ground though! And now there starts to be a few more bio-related tools and toolkits out there, including:
- https://github.com/vertgenlab/gonomics
- https://github.com/biogo/biogo
- https://github.com/shenwei356/bio
... except from there being some really popular bio tools written in Go, like:
- https://github.com/shenwei356/seqkit
-
Help with understanding awk code
You could also check out tools specialized for FASTA processing like https://github.com/shenwei356/seqkit and https://github.com/lh3/seqtk
-
What are some good examples of well-engineered bioinformatics pipelines?
Seqkit - thoroughly maintained with extensive tutorials and benchmarking info - https://github.com/shenwei356/seqkit
What are some alternatives?
juicer - A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
seqtk - Toolkit for processing sequences in FASTA/Q formats
sv-callers - Snakemake-based workflow for detecting structural variants in genomic data
sage - Proteomics search & quantification so fast that it feels like magic
rush - A cross-platform command-line tool for executing jobs in parallel
veba - A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.