Independent Teams

Workflows from the Industrial Biotechnology Innovation and Synthetic Biology Accelerator (IBISBA 1.0) project, which is funded by the European Union Horizon 2020 program INRAIA-02 under grant agreement 730976.

The workflows also appear on https://hub.ibisba.eu

An open infrastructure for exploring new horizons for research on microbial communities.

A team to try the workflow hub and register workflows

Collection of workflows and tools to facilitate the assembly of (Italian) SARS-CoV-2 genomes and deposition of relevant data in INDSC sequence databases

Poster and presentation video by Ambarish Kumar

Workflow for Metagenomics from raw reads to annotated bins.

Steps:

• workflow_quality.cwl:

• FastQC (control)

• fastp (trimming)

• Kraken2 (Taxonomic Read Classification

• SPAdes (Assembly)

• QUAST (Assembly quality report)

• BBmap (Read mapping to assembly)

• samtobam (sam to indexed bam)

• metabatContigDepths (jgisummarizebamcontigdepths)

• MetaBat2 (binning)

Workflow for read quality control and trimming.

Steps:

• FastQC (read quality control)

• fastp (read quality trimming)

• bbduk used for rrna filtering

Workflow 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)