Recently published apps

We have just published the following apps in our Public Apps gallery:

• TwoSampleMR, a tool that performs Mendelian randomization testing for a given exposure-outcome pair. It is a wrapper around the TwoSampleMR R package and uses summary statistics data for making causal inference.
• CCS, a tool that combines multiple subreads of the same SMRTbell molecule and outputs one highly accurate consensus sequence.
• lima, a tool used with PacBio single-molecule sequencing data for barcode and primer sequences identification.
• PacBio Flowcell Data Processing, a workflow that can be used to process PacBio CCS or CLR data in preparation for variant calling.
• PacBio CCS or CLR WGS Variant Calling workflow that can be used to call structural variants in PacBio CCS or CLR data. The workflow can also call small variants in CCS data using Clair3.
• WARP WGS DRAGEN-GATK Single Sample, a WGS single sample processing workflow with DRAGMAP and GATK.
• WARP TargetedSomaticSingleSample Pipeline, designed for somatic human targeted sequencing data analysis. The workflow takes human single sample uBAM input files which will be converted into FASTQ reads and mapped to a reference file. The obtained alignment files will be passed to the quality control tools, calculating and producing different quality metrics. Output targeted somatic alignment files can be further used for variant calling or other analyses by different tools/pipelines, while metrics outputs can give various quality and statistical calculations about input data and the produced alignment file.

Marko Marinkovic