If an extended scaffold cannot be joined to another scaffold after a few rounds of extension it may be worth testing for an additional scaffold (possibly small, thus easily missed by binning) by searching the full metagenome for overlaps. It should be noted that read by read scaffold extension is very time-consuming. This process of extending, joining and remapping may continue until all fragments comprise a single circularized sequence. “Scaffolds within a bin that do not overlap at the start of curation may be joined after one or more rounds of scaffold extension. Scaffold extension uses the paired-end reads mapped to a given scaffold to extend its ends, (1) to get the complete sequence of a protein-coding gene or rRNA gene at the ends, (2) to assemble it with another scaffold based on overlap sequences at the end, (3) to obtain a complete genome of bacteria, archaea, virus, phage, etc. Here we will detail the two primary strategies we commonly use to improve MAGs to completion: scaffold extension and gap closing. Our paper provides a step-by-step procedure of how to curate a draft MAG generated by manual or automatic binning tools to prevent errors (e.g., misbinned scaffolds, local assembly errors), close scaffolding gaps and thus generate high-quality or complete MAGs (CMAGs). The CGM paper summarizes the history of genome-resolved metagenomics, with examples from publications, to show the necessity of genome binning and manual curation of MAGs to avoid misleading conclusions. Please cite this publication if you follow the procedures described here for your analyses. These strategies are described in our recent paper entitled “Accurate and Complete Genomes from Metagenomes” ("CGM" for short hereafter), which is available at. For any questions about the methods described below, please contact us via email ( purpose of this post is to describe step-by-step procedure for scaffold extension and gap closing to dramatically improve the quality of metagenome-assembled genomes (MAGs). A post by Lin-Xing Chen, Karthik Anantharaman, Alon Shaiber, A.
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