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Our list of good practices in (meta)genome assembly

Lex Nederbragt (corr) et al.

  • talk to the bioinformatician(s) before doing anything
  • QC your reads with fastqc, preqc (khmer?)
  • try different programs for assembly (not too many, but more than one)
  • map the reads back to the assembly and use QC/Validation programs
  • Use orthogonal data for QC/Validation * known genes * CEGMA/Phylosift * RNA-seq data * linkage map data/optical mapping data/fosmids or BAC data
  • do blobology to figure out what you actually assembled (for any genome/metagenome)
  • make reads, mapped reads and validation results available upon release of the genome (or before)
  • make the genome assembly work reproducible

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LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons - 0 License (CC0) -- fork @ github. Presentations (PPT/PDF) and PDFs are the property of their respective owners and are under the terms indicated within the presentation.

Development and posting of this material, and the associated workshop, were supported by Grant Number R25HG006243 from the National Human Genome Research Institute and an NSF OCI supplement to NSF DBI-0939454.

© Copyright 2013, Holly Bik, C. Titus Brown, Nick Loman, Lex Nederbragt, Jared Simpson. Created using Sphinx 1.1.3.

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