On the path to reference genomes for all biodiversity: lessons learned and laboratory protocols created in the Sanger Tree of Life core laboratory over the first 2000 species
Howard, C.; Denton, A.; Jackson, B.; Bates, A.; Jay, J.; Yatsenko, H.; Raman, P. S.; Thomas, A.; Oatley, G.; do Amaral, R. V.; Göktan, Z. E.; Gomez, J. P. N.; Clayton Lucey, I.; Sinclair, E.; Quail, M. A.; Blaxter, M.; Howe, K.; Lawniczak, M.
Show abstract
Since its inception in 2019, the Tree of Life programme at the Wellcome Sanger Institute has released high-quality, chromosomally-resolved reference genome assemblies for over 2000 species. Tree of Life has at its core multiple teams, each of which are responsible for key components of the genome engine. One of these teams is the Tree of Life core laboratory, which is responsible for processing tissues across a wide range of species into high quality, high molecular weight DNA and intact RNA, and preparing tissues for Hi-C. Here, we detail the different workflows we have developed to successfully process a wide variety of species, covering plants, fungi, chordates, protists, arthropods, meiofauna and other metazoa. We summarise our success rates and describe how to best apply and combine the suite of current protocols, which are all publicly available at protocols.io.
Matching journals
The top 4 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Barcode 100K Specimens: In a Single Nanopore Run 95%
- Towards large-scale museomics projects: a cost-effective and high-throughput extraction method for obtaining historical DNA from museum insect specimens 94%
- Identification and quantification of chimeric sequencing reads in a highly multiplexed RAD-seq protocol 94%
Similar papers in this journal
- Can we use it? On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing 94%
- Comparative analysis of novel MGISEQ-2000 sequencing platform vs Illumina HiSeq 2500 for whole-genome sequencing 94%
- Liquid biopsies for omics-based analysis in sentinel mussels. 93%
Similar papers in this journal
- Consistent ultra-long DNA sequencing with automated slow pipetting 95%
- Fine-Tuning GBS Data with Comparison of Reference and Mock Genome Approaches for Advancing Genomic Selection in Less Studied Farmed Species 94%
- Flexible, Production-Scale, Human Whole Genome Sequencing On A Benchtop Sequencer 94%
Similar papers in this journal
- Rapid and real-time identification of fungi up to the species level with long amplicon Nanopore sequencing from clinical samples. 91%
- MINTyper: An outbreak-detection method for accurate and rapid SNP typing of clonal clusters with noisy long reads 90%
- A modified dual preparatory method for improved isolation of nucleic acids from laser microdissected fresh-frozen human cancer tissue specimens 89%
Similar papers in this journal
- Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American killifish from the Fundulus genus 96%
- Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing 94%
- dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology 94%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.