iwc

A workflow for the analysis of pox virus genomes sequenced as half-genomes (for ITR resolution) in a tiled-amplicon approach

Automated inference of stable isotope incorporation rates in proteins for functional metaproteomics

Generate Nx and Size plot for multiple assemblies

Inputs

Collection of fasta files. The name of each item in the collection will be used as label for the Nx and Size plots.

Outputs

1. Nx plot
2. Size plot

This workflow takes as input a SRA_manifest from SRA Run Selector and will generate one fastq file or fastq pair of file for each experiment (concatenated multiple runs if necessary). Output will be relabelled to match the column specified by the user.

Antimicrobial resistance gene detection from assembled bacterial genomes

Assembly of bacterial paired-end short read data with generation of quality metrics and reports

Short paired-end read analysis to provide quality analysis, read cleaning and taxonomy assignation

This workflow takes as input a list of paired-end fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools.

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.

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.

This workflow takes as input a collection of paired fastq. It will remove bad quality and adapters with cutadapt. Map with Bowtie2 end-to-end. Will remove reads on MT and unconcordant pairs and pairs with mapping quality below 30 and PCR duplicates. Will compute the pile-up on 5' +- 100bp. Will call peaks and count the number of reads falling in the 1kb region centered on the summit. Will compute 2 normalization for coverage: normalized by million reads and normalized by million reads in peaks. ...

This workflow takes as input a list of single-reads fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools.

Microbiome - Taxonomy Profiling

Nanopore datasets analysis - Phylogenetic Identification - antibiotic resistance genes detection and contigs building

Microbiome - Variant calling and Consensus Building

Microbiome - QC and Contamination Filtering

Pathogens of all samples report generation and visualization

Annotation of an assembled bacterial genomes to detect genes, potential plasmids, integrons and Insertion sequence (IS) elements.

This workflow

• Reconstruct phylogeny (insert fragments in a reference)
• Alpha rarefaction analysis
• Taxonomic analysis