PopMAG: Automated Population Genetics Analysis of MAGs

nf-core/variantbenchmarking is designed to evaluate and validate the accuracy of variant calling methods in genomic research. Initially, the pipeline is tuned well for available gold standard truth sets (for example, Genome in a Bottle and SEQC2 samples) but it can be used to compare any two variant calling results. The workflow provides benchmarking tools for small variants including SNVs and INDELs, Structural Variants (SVs) and Copy Number Variations (CNVs) for germline and somatic analysis.

Pathogensurveillance is a population genomics pipeline for pathogen identification, variant detection, and biosurveillance. The pipeline accepts paths to raw reads for one or more organisms and creates reports in the form of an interactive HTML document. Significant features include the ability to analyze unidentified eukaryotic and prokaryotic samples, creation of reports for multiple user-defined groupings of samples, automated discovery and downloading of reference assemblies from NCBI RefSeq, and rapid initial identification based on k-mer sketches followed by a more robust multi gene phylogeny and SNP-based phylogeny.

A pipeline for preprocessing short and long sequencing reads, built with Nextflow.

VENAE is a bioinformatic workflow that rapidly identifies bacterial and fungal organisms and their antimicrobial resistance (AMR) determinants from positive blood cultures using Oxford Nanopore long-read sequencing. It generates a clinician-friendly HTML report to support timely clinical decision-making.

Ultra-fast, sensitive search and clustering suite for protein and nucleotide sequence sets.

Workflow library embedded in the Go programming language, focusing on supporting complex workflow constructs, compiling to a single binary, providing powerful file naming and comprehensive audit reports for every output