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