{"repo":"nf-core/multiplesequencealign","free":true,"listed":false,"github":"https://github.com/nf-core/multiplesequencealign","clone":"git clone https://github.com/nf-core/multiplesequencealign.git","description":"A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.","language":"Nextflow","stars":41,"topics":["nextflow","nf-core","pipeline","workflow"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction Use nf-core/multiplesequencealign to: 1. Deploy one (or many) of the most popular Multiple Sequence Alignment (MSA) tools. 2. Benchmark MSA tools (and their inputs) using various metrics. Main steps: Inputs summary (Optional) Computation of summary statistics on the input files (e.g., average sequence similarity across the input sequences, their length, pLDDT extraction if available). Guide Tree (Optional) Renders a guide tree with a chosen tool (list available in usage ). Some aligners use guide trees to define the order in which the sequences are aligned. Align (Required) Aligns the sequences with a chosen tool (list available in usage ). Evaluate (Optional) Evaluates the generated alignments with different metrics: Sum Of Pairs (SoP), Total Column score (TC), iRMSD, Total Consistency Score (TCS), etc. Report (Optional) Reports the collected information of the runs in a Shiny app and a summary table in MultiQC. Optionally, it can also render the Foldmason MSA visualization in HTML format. More introductory material: bytesize talk, nextflow summit talk, poster. Usage [!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data. Quick start - test run To get a feeling of what the pipeline does, run: (You don't need to download or provide any file, try it!) and if you want to see how a more complete run looks like, you can try: How to ","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/multiplesequencealign/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."}