Our list of good practices in (meta)genome assembly
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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