Starred repositories
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
Workflow management with Nextflow and nf-core
A curated collection of Nextflow implementation patterns
PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. This is a comprehensive upd…
Read-based phasing of genomic variants, also called haplotype assembly
regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Toolkit for preparing genomes for submission to NCBI
A small pipeline for assembling mitochondrial genomes and filtering reads prior to assembly.
Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.
De novo assembler for single molecule sequencing reads using repeat graphs
A pipeline for assemble chroloplast genome using short/long reads
scripts and intermediate files used to annotate TEs in Jiao et al.
Applied Computational Genomics Course at UU: Spring 2020
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