sv-callers
hecatomb
| sv-callers | hecatomb | |
|---|---|---|
| 1 | 1 | |
| 71 | 41 | |
| - | - | |
| 2.9 | 8.5 | |
| 4 months ago | 2 months ago | |
| Python | Python | |
| Apache License 2.0 | MIT License |
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sv-callers
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Do you know how to get CNVs out of WES data sorted.bam files? (Free)
Generally, you have multiple ways to tackle this kind of a problem. For short read sequencing you have two types of CNV detection - readdepth based and paired-end based. CNVpytor (CNVnator) for example, is the former. You also have manta and lumpy. A lot of good pipelines use more than one SV caller and integrate them. For example: https://github.com/GooglingTheCancerGenome/sv-callers
hecatomb
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Viral Metagenomics - assembly/annotation issues
Try this https://github.com/shandley/hecatomb
What are some alternatives?
gatk4-genome-processing-pipeline-azure - Workflows used for processing whole genome sequence data + germline variant calling.
pypsa-eur - PyPSA-Eur: A Sector-Coupled Open Optimisation Model of the European Energy System
metaGEM - :gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
covalent - Pythonic tool for orchestrating machine-learning/high performance/quantum-computing workflows in heterogeneous compute environments.
cookiecutter-snakemake-workflow - A cookiecutter template for Snakemake workflows
aviary - A hybrid assembly and MAG recovery pipeline (and more!)
rna-seq-kallisto-sleuth - A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
zarp - The Zavolab Automated RNA-seq Pipeline
galaxy - Data intensive science for everyone.
SigProfilerExtractor - SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.