{"repo":"nf-core/hgtseq","free":true,"listed":false,"github":"https://github.com/nf-core/hgtseq","clone":"git clone https://github.com/nf-core/hgtseq.git","description":"A pipeline to investigate horizontal gene transfer from NGS data","language":"Nextflow","stars":27,"topics":["nextflow","nf-core","pipeline","workflow","horizontal-gene-transfer","ngs","taxonomies","bwa-mem","bwa-mem2","fastqc"],"license":"MIT","category":"workflow-automation","readme_excerpt":"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 manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the nf-core website. Functionality Overview A graphical view of the pipeline can be seen below. Pipeline summary 1. Re","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/hgtseq/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}