https://github.com/seqan/knime_seqan_workflows
KNIME example workflows for NGS data analysis with SeqAn apps.
https://github.com/seqan/knime_seqan_workflows
Last synced: 4 months ago
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KNIME example workflows for NGS data analysis with SeqAn apps.
- Host: GitHub
- URL: https://github.com/seqan/knime_seqan_workflows
- Owner: seqan
- Created: 2014-03-26T10:06:45.000Z (about 12 years ago)
- Default Branch: master
- Last Pushed: 2016-05-12T15:46:19.000Z (about 10 years ago)
- Last Synced: 2026-02-11T02:26:35.026Z (4 months ago)
- Size: 58.8 MB
- Stars: 5
- Watchers: 8
- Forks: 5
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
SeqAn Community Workflows
=========================
KNIME example workflows for NGS data analysis with SeqAn apps. Here we host and share community workflows.
Please read the howto at http://seqan.readthedocs.io/en/master/Tutorial/Workflows/UseSeqAnNodesInKnime.html first about how to integrate
SeqAn nodes into KNIME and how to use or contribute workflows.
Workflows
---------
### Variant Calling ###
- [Variant Calling with SnpStore](variant_calling_snpstore_workflow)
- Two variant calling workflows based on the read mapper RazerS 3 and the variant caller SnpStore.
- [Variant Calling with mpileup](variant_calling_bwa_workflow)
- A variant calling workflow based on the read mapper BWA and samtools mpileup for variant calling.
### BS-Seq Analysis ###
- [BS-Seq Analysis with bs-tools](bs_seq_analysis_workflow)
- A workflow for BS-Seq data analysis, from bisulfite read mapping to SNP and methylation level calling at single-nucleotide resolution.
### Metagenomics ###
- [GASiC workflow](metagenomics_gasic_workflow)
- Genome Abundance Similarity Correction workflow.
### Benchmarking ###
- [Rabema Example Workflow](rabema_example_workflow)
- A workflow to benchmark the sensitivity of read mappers.
Contact
-------
If you have questions feel free to contact the SeqAn mailing list at seqan-dev@lists.fu-berlin.de