Workflows
What is a Workflow?Filters
Tests We assume the identifiers of the input list are like: sample_name_replicateID. The identifiers of the output list will be: sample_name
RepeatMasking Workflow
This workflow uses RepeatModeler and RepeatMasker for genome analysis.
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RepeatModeler is a software package for identifying and modeling de novo families of transposable elements (TEs). At the heart of RepeatModeler are three de novo repeat search programs (RECON, RepeatScout and LtrHarvest/Ltr_retriever) which use complementary computational methods to identify repeat element boundaries and family relationships from sequence data.
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RepeatMasker is a program that analyzes ...
Racon polish with long reads, x4
Downloads fastq files for sequencing run accessions provided in a text file using fasterq-dump. Creates one job per listed run accession.
This workflow takes as input SR BAM from ChIP-seq. It calls peaks on each replicate and intersect them. In parallel, each BAM is subsetted to smallest number of reads. Peaks are called using both subsets combined. Only peaks called using a combination of both subsets which have summits intersecting the intersection of both replicates will be kept.
This workflow takes as input a collection of paired fastqs. Remove adapters with cutadapt, map pairs with bowtie2. Keep MAPQ30 and concordant pairs. MACS2 for paired bam.
This workflow takes as input a collection of fastqs (single reads). Remove adapters with cutadapt, map with bowtie2. Keep MAPQ30. MACS2 for bam with fixed extension or model.
A workflow for the analysis of pox virus genomes sequenced as half-genomes (for ITR resolution) in a tiled-amplicon approach
Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring
This workflow take as input a collection of paired fastq. Remove adapters with cutadapt, map pairs with bowtie2 allowing dovetail. Keep MAPQ30 and concordant pairs. BAM to BED. MACS2 with "ATAC" parameters.
