Workflows
What is a Workflow?Query
Created At
Updated At
Workflow type
Common Workflow Language13
Tag
Genomics4
Metagenomics4
Alignment2
Amplicon2
Assembly2
binning2
Classification2
CWL2
illumina2
kallisto2
nanopore2
16S1
bowtie21
carveme1
featurecounts1
filtering1
GEM1
ITS1
memote1
metagenome1
microbial1
nonspliced1
quality1
rna1
rna-seq1
RNASEQ1
STAR1
Transcriptomics1
More...
Team
UNLOCK13
Space
Independent Teams13
Topic annotations
Metagenomics5
Metagenomic sequencing3
Bioinformatics2
Sequence analysis2
Sequence assembly2
Sequencing2
Data quality management1
More...
13
Workflows visible to you, out of a total of 13
Work-in-progress
Workflow for NonSpliced RNAseq data with multiple aligners.
Steps:
- workflow_quality.cwl:
- FastQC (control)
- fastp (trimming)
- bowtie2 (read mapping)
- sam_to_sorted-bam
- featurecounts (transcript read counts)
- kallisto (transcript [pseudo]counts)
Download
Stable
Amplicon analysis workflow using NG-Tax
Steps:
- Quality control on the reads
- Execute NGTax for ASV detection and classification
For more information about NG-Tax 2.0 have a look at https://doi.org/10.3389/fgene.2019.01366
Type: Common Workflow Language
Creators: Jasper Koehorst, Bart Nijsse, Jesse van Dam, Peter Schaap,
Submitter: Jasper Koehorst
Work-in-progress
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
