gatk4-genome-processing-pipeline-azure
Workflows used for processing whole genome sequence data + germline variant calling. (by microsoft)
spades
SPAdes Genome Assembler (by ablab)
gatk4-genome-processing-pipeline-azure | spades | |
---|---|---|
4 | 4 | |
7 | 677 | |
- | 3.5% | |
0.0 | 9.3 | |
2 months ago | 1 day ago | |
wdl | C++ | |
BSD 3-clause "New" or "Revised" License | GNU General Public License v3.0 or later |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
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.
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
Posts with mentions or reviews of gatk4-genome-processing-pipeline-azure.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-04-05.
- What are some good examples of well-engineered bioinformatics pipelines?
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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.
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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.
spades
Posts with mentions or reviews of spades.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-05-25.
- my friend showed me his code, thees are all functions
- What are some good examples of well-engineered bioinformatics pipelines?
-
Genome analysis cost
If you do DNA sequencing and receive the sequencing files as fastq files (normal from sequencing) then spades to assemble the genome, then put it through PROKKA to annotate it. Here's a beginners guide, the most difficult part is downloading the programs onto your laptop.
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Is it possible to assemble a complete bacterial genome using short reads?
MetaSpades has a cool option to hybrid reform contigs using short and long reads so you could pair short read data and long read data (PacBio/ONT) to get the best hybrid assembly with high throughput and long reference reads for resolving the reassembling. https://github.com/ablab/spades
What are some alternatives?
When comparing gatk4-genome-processing-pipeline-azure and spades you can also consider the following projects:
juicer - A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
prokka - :zap: :aquarius: Rapid prokaryotic genome annotation
sv-callers - Snakemake-based workflow for detecting structural variants in genomic data
mag - Assembly and binning of metagenomes
sage - Proteomics search & quantification so fast that it feels like magic
seqkit - A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
veba - A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
bwa - Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)