zarp
sv-callers
| zarp | sv-callers | |
|---|---|---|
| 1 | 1 | |
| 29 | 71 | |
| - | - | |
| 7.2 | 2.9 | |
| 2 months ago | 3 months ago | |
| Python | Python | |
| Apache License 2.0 | Apache License 2.0 |
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zarp
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
What are some alternatives?
atlas - ATLAS - Three commands to start analyzing your metagenome data
gatk4-genome-processing-pipeline-azure - Workflows used for processing whole genome sequence data + germline variant calling.
RNA-seq-analysis - RNAseq analysis notes from Ming Tang
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
bioawk - BWK awk modified for biological data
covalent - Pythonic tool for orchestrating machine-learning/high performance/quantum-computing workflows in heterogeneous compute environments.
aviary - A hybrid assembly and MAG recovery pipeline (and more!)
PyDESeq2 - A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
hecatomb - hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
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.