Workflows

The workflow main goal is to align DNA-Seq read files with BWA-MEM , with optional adapter trimming, UMI consensus calling, duplicate marking. Finally it runs Multi QC to gather tool metrics. The workflow was designed to be run in the SeqUIa (http://cfb.ceitec.muni.cz/sequia) application.

The workflow main goal is to run divers tools to obtain alignment quality metrics from RNA-Seq, DNA-Seq, and ChIP-Seq using Picard, Qualimap, Samtools, dupradar, biotype analysis, FastQ Screen, RSeQC or Phantom peak. Finally it runs Multi QC to gather tool metrics. The workflow was designed to be run in the SeqUIa (http://cfb.ceitec.muni.cz/sequia) application.

The workflow main goal is to count reads aligned or pseudo-aligned to reference genome annotation using featureCount, HTSeq-count, RSEM, Kallisto or Salmon. Finally it runs Multi QC to gather tool metrics. The workflow was designed to be run in the SeqUIa (http://cfb.ceitec.muni.cz/sequia) application.

The workflow main goal is to align RNA-Seq read files with STAR and to check for duplicates using either Picard Markduplicates or UMI-tools. Finally it runs Multi QC to gather tool metrics. The workflow was designed to be run in the SeqUIa (http://cfb.ceitec.muni.cz/sequia) application.

The workflow main goal is to quality trim reads of input fastq files and to remove adaptors. It can also run Biobloom tools and species detector in order to check for contamination. Finally it runs fastq QC to obtain quality check after trimming. The workflow was designed to be run in the SeqUIa (http://cfb.ceitec.muni.cz/sequia) application.

The workflow main goal is to check the quality of input fastq files after sequencing and demultiplexing. Optionaly it can check for most abundant adaptor sequences. It can also merge fastq files belonging from the same samples after resequencing prior to quality check. The workflow was designed to be run in the SeqUIa (http://cfb.ceitec.muni.cz/sequia) application.