nf-core
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- A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered
- Assembly and binning of metagenomes
- Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
- Longread PacBio sequencing processing for WGS and PureTarget
- Config files used to define parameters specific to compute environments at different Institutions
- A fully reproducible and state-of-the-art ancient DNA analysis pipeline
- Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.
- Pipeline dedicated to finding the most stable genes among a single or multiple expression dataset(s). It is useful in particular for finding the most suitable qPCR reference genes for a specific species.
- Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results
- Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
- Parallelised and automated construction of metagenomic classifier databases of different tools
- Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
nanostring
PublicAn analysis pipeline for Nanostring nCounter expression data.- Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing