nf-core/hgtseq

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Introduction nf-core/hgtseq is a bioinformatics best-practice analysis pipeline built to investigate horizontal gene transfer from NGS data. The pipeline uses metagenomic classification of paired-read alignments against a reference genome to identify the presence of non-host microbial sequences within read pairs, and to infer potential integration sites into the host genome. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable...