Literature

Getting started

Ten steps to get started in Genome Assembly and Annotation: How to get started with a de novo assembly project.

Assembly polishing

Errors in long-read assemblies can critically affect protein prediction: A paper on the nature of errors in long-read assemblies.

Assembly validation

Human contamination in bacterial genomes has created thousands of spurious proteins: The importance of contamination removal.

Advanced Assembly material.

Plasmid detection and assembly in genomic and metagenomic data sets: Background material for plasmid assembly.

Telomere-to-telomere assembly of a complete human X chromosome: Considerations regarding assembly and polishing of repetitive regions.

HINGE: long-read assembly achieves optimal repeat resolution: Assembly theory for resolving repeats.

Alternative methodology

Chromosome-length haplotigs for yak and cattle from trio binning assembly of an F1 hybrid: A preprint describing breeding a highly heterozygous individual, and sequencing both parents and offspring to assemble a near complete diploid assembly.