nf-core
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Public- Assembly and binning of metagenomes
- Config files used to define parameters specific to compute environments at different Institutions
tools
Public- A fully reproducible and state-of-the-art ancient DNA analysis pipeline
metatdenovo
PublicAssembly 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.
pairgenomealign
PublicPairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the resultspathogensurveillance
Public- 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
dualrnaseq
PublicAnalysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.pixelator
PublicPipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)mhcquant
Publiccreatetaxdb
PublicParallelised and automated construction of metagenomic classifier databases of different toolspangenome
Publictaxprofiler
PublicHighly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic datamultiplesequencealign
Publicnanostring
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
references
Publicnf-core/references is a bioinformatics pipeline that build references, for multiple use casesreferences-assets
Public