sv-callers
galaxy
| sv-callers | galaxy | |
|---|---|---|
| 1 | 4 | |
| 71 | 1,320 | |
| - | 1.8% | |
| 2.9 | 10.0 | |
| 3 months ago | 1 day ago | |
| Python | Python | |
| Apache License 2.0 | GNU General Public License v3.0 or later |
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.
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
galaxy
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Need for GUIs for bioinformatic tools?
Maybe it would help you to look at the galaxy project: GitHub main site
- BIOINFORMATICS PROJECT
- Any bioinfo open source projects looking for contributors?
- Developed a new kind of dual extruder system on fully custom built 3D printer
What are some alternatives?
gatk4-genome-processing-pipeline-azure - Workflows used for processing whole genome sequence data + germline variant calling.
nextflow - A DSL for data-driven computational pipelines
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
Biopython - Official git repository for Biopython (originally converted from CVS)
covalent - Pythonic tool for orchestrating machine-learning/high performance/quantum-computing workflows in heterogeneous compute environments.
deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
aviary - A hybrid assembly and MAG recovery pipeline (and more!)
fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
zarp - The Zavolab Automated RNA-seq Pipeline
sarek - Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
hecatomb - hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
galaxy_ng - Ansible Galaxy Server - Issues on https://forum.ansible.com Docs on https://galaxy-ng.readthedocs.io/