Bart Nijsse
SEEK ID: https://workflowhub.eu/people/84
Location:
Netherlands
Expertise: Not specified
Tools: Not specified
https://orcid.org/0000-0001-9524-5964
Their tagsRelated items
A space managed by WorkflowHub administrators for teams that don't want/need to manage their own space.
Teams: IBISBA Workflows, NMR Workflow, UNLOCK, NanoGalaxy, Galaxy Climate, PNDB, IMBforge, COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource, LBI-RUD, Nick-test-team, usegalaxy-eu, Italy-Covid-data-Portal, UX trial team, Integrated and Urban Plant Pathology Laboratory, SARS-CoV-2 Data Hubs, lmjxteam2, Australian BioCommons, virAnnot pipeline, Ay Lab
Web page: Not specified
An open infrastructure for exploring new horizons for research on microbial communities.
Workflow for read quality control and trimming.
Steps:
FastQC (read quality control)
fastp (read quality trimming)
bbduk used for rrna filtering
DownloadWorkflow for NonSpliced RNAseq data with multiple aligners.
Steps:
workflow_quality.cwl:
FastQC (control)
fastp (trimming)
bowtie2 (read mapping)
samtosorted-bam
featurecounts (transcript read counts)
kallisto (transcript [pseudo]counts)
Workflow for Spliced RNAseq data
Steps:
workflow_quality.cwl:
FastQC (Read Quality Control)
fastp (Read Trimming)
STAR (Read mapping)
featurecounts (transcript read counts)
kallisto (transcript [pseudo]counts)
Workflow to build different indices for different tools from a genome and transcriptome.
This workflow expects an (annotated) genome in GBOL ttl format.
Steps:
SAPP: rdf2gtf (genome fasta)
SAPP: rdf2fasta (transcripts fasta)
STAR index (Optional for Eukaryotic origin)
bowtie2 index
kallisto index
