This work has been peer reviewed in GigaScience, which carries out open, named peer-review. These reviews are published under a CC-BY 4.0 license and were as follows:

Reviewer 1: Karen Ross http://dx.doi.org/10.5524/REVIEW.102747 Reviewer 2: Carlos P. Cantalapiedra http://dx.doi.org/10.5524/REVIEW.102749

This work has been peer reviewed in GigaByte, which carries out open, named peer-review. These reviews are published under a CC-BY 4.0 license and were as follows:

Review 1. Walter Wolfsberger Is the language of sufficient quality? Yes.

Is the data all available and does it match the descriptions in the paper? Yes.

Is the data and metadata consistent with relevant minimum information or reporting standards?

Comment: The accession number for GigaDB provided in the paper does not yield any results in the GigaDB search. Using the species name works though.

Is the data acquisition clear, complete and methodologically sound?

Comment: Although it is clear in the paper that a significant portion of data was discarded during the early QC step, there is no indication of the reason for it, or the nature of the problem that was encountered. For total in the paper, the research group produced 396 Gb of raw sequence(211 Short insert and 185 long insert libraries) out of which only 180(130 Gb Short insert and never mentioned 55Gb Long insert) were used later on for the assembly. Upon a single library FastQC analysis I have encountered extreme levels of sequence duplication that might indicate the libraries were not diverse or there was a PCR-artifact(like overamplification), that might have lead to this low-quality initial data. The parameters for tool SoapNuke, used in early QC are not defined.

Is there sufficient detail in the methods and data-processing steps to allow reproduction?

Is there sufficient data validation and statistical analyses of data quality? Yes.

Is the validation suitable for this type of data?

Comments: The assembly followed a logical order, with appropriate tools used at every step.

Is there sufficient information for others to reuse this dataset or integrate it with other data?

Comment: Although the resulting assembly was of moderate quality(highly fragmented, but good BUSCO score), a randomly picked library showed a really high duplication rates for sequencing, which indicates that there might be problems for future data reuse. Addressing these issues or at least acknowledging them would benefit the whole report and the dateset.

Additional Comments:

I don't think physical coverage is used widely in genome assembly as of now, as given the mate-pair reads nature - it inflates this statistics. I would put the resulting assembly statistics in a table, including all of the metrics(N50, N of Contigs, N of Scaffolds, Average Contig length and etc.) adding BUSCO score to the table, as the current formatting is not readable.  

Review 2. Nandita Mullapudi Is the language of sufficient quality? Yes.

Is the data all available and does it match the descriptions in the paper? Yes.

Is the data and metadata consistent with relevant minimum information or reporting standards?

Comment: I am unaware of defined reporting standards for assembly reports, however, all sample preparation, data generation and analysis methods have been described in adequate amount of detail.

Is the data acquisition clear, complete and methodologically sound? Yes.

Is there sufficient detail in the methods and data-processing steps to allow reproduction?

Comment: Following additional details would help to enable reproduction: (1) Parameters used for data pre-processing using SOAPnuke, as well as related adapter sequences etc. These would be necessary to reproduce the data clean up step. (2) Memory, processor and time details of computational resource used for assembly (3) Was Platanus assembly attempted using different parameters, how were the parameters reported in the paper arrived at? (4) For gene prediction, several vertebrate sequences were used, the details/source of these reference sequences are missing.

Is there sufficient data validation and statistical analyses of data quality?

Comments: 1) One approach to validating an assembly would be to use more than one assembly tool and compare the results. (This may or may not be within the scope of this study.) 2) With respect to the validation performed by mapping back paired end reads to the assembly, there is no discussion of the ~14% of paired end reads that did not map back in the expected orientation. Would tools like REAPR (https://www.sanger.ac.uk/science/tools/reapr) or SEQuel (https://bix.ucsd.edu/SEQuel/man.html) be appropriate to address this? (given the high level of heterozygosity in L. d. dumerilii as reported here).

Is the validation suitable for this type of data? Yes.

Is there sufficient information for others to reuse this dataset or integrate it with other data?

Comments: It may also be helpful to make available the set of cleaned reads, to enable reproduction of the assembly pipeline.

This work has been peer reviewed in GigaScience, which carries out open, named peer-review. These reviews are published under a CC-BY 4.0 license and were as follows:

Reviewer 1. (Eric Van Nostrand) http://dx.doi.org/10.5524/REVIEW.102771 Reviewer 2. (Nejc Haberman) http://dx.doi.org/10.5524/REVIEW.102769<br> Reviewer 3. (William Lai) http://dx.doi.org/10.5524/REVIEW.102770

See the video abstract on the GigaScience youtube channel: https://youtu.be/29vOiwQwj_U

See a video abstract in the GigaScience youtube channel; https://youtu.be/mrqxyk1K2eU

See the first Update in GigaByte https://doi.org/10.46471/gigabyte.24

There is a protocol for this now listed in protocols.io http://dx.doi.org/10.17504/protocols.io.bpwxmpfn

See more on how this works in GigaBlog http://gigasciencejournal.com/blog/codecheck-certificate/

Read more in GigaBlog http://gigasciencejournal.com/blog/idseq-infectious-disease-detectives/ and the NYT here https://www.nytimes.com/2021/06/03/magazine/metagenomic-sequencing.html?fbclid=IwAR2RlEvW7OhD_JQxnVasIDu8bJYano2I9Vv-ihX9Choa2FbHNCOOo9s1BZI

Read more in this GigaBlog post on the paper http://gigasciencejournal.com/blog/cone-snail-genome-sheds-light-on-venom-evolution/

See the previous GigaScience paper looking at high-throughput identification of conotoxins using multi-transcriptome sequencing https://doi.org/10.1186/s13742-016-0122-9

Read more on this evolution in this Q&A with the authors http://gigasciencejournal.com/blog/play-it-again-samtools/

Read more on these developments in the Q&A with the authors http://gigasciencejournal.com/blog/play-it-again-samtools/

What about video abstracts (e.g. like https://youtu.be/8T-lwGEGlGs) or video summaries (e.g. like https://youtu.be/z_WkZzhCpJw)"?

e.g. winning the 2018 PROSE Award for Innovation in Publishing http://gigasciencejournal.com/blog/gigascience-prose-award-for-innovation/

See also the data posted in GigaDB in 2012

And new data here http://dx.doi.org/10.5524/100875

See the new generation chromosome scale pacific oyster reference published in March 2021 https://doi.org/10.1093/gigascience/giab020

Find out more in this GigaBlog posting on the project http://gigasciencejournal.com/blog/rickettsia-bacteria-to-rule-them-all/

For more on the African Orphan Crops Consortium see GigaBlog http://gigasciencejournal.com/blog/democratising-data-aocc/

For more on how this went and an update on where the platform has developed to in Feb 2021 can be viewed in this video from CWLcon2021 https://youtu.be/vV4mmH5eN58

And see also the coverage in the WSJ https://www.wsj.com/articles/SB10000872396390444840104577551433143153716

New migrations to the UK are being tracked by citizen science projects to see if this is related to climate change http://srs.britishspiders.org.uk/portal/p/Wasp+Spider

Can watch a video abstract with the author here https://youtu.be/8T-lwGEGlGs

See the write-up by the Earlham Institute for more on how this training is going on

See coverage in Wired https://www.wired.com/story/a-disease-tracker-backed-by-gates-and-zuckerberg-tackles-covid-19/

For more background see GigaBlog http://gigasciencejournal.com/blog/idseq-infectious-disease-detectives/

Which has now become NISO CRediT (Contributor Roles Taxonomy), see http://credit.niso.org/

Sequencing data is also in NCBI via BioProject: PRJNA576514 and proteomics data is in PRIDE: PXD018943

This paper (and data type) gets a mention in GigaBlog http://gigasciencejournal.com/blog/guest-blog-challenges-and-opportunities-with-sharing-neuroimaging-data/

Part of our fMRI series: https://academic.oup.com/gigascience/pages/fmri_advances_and_challenges

Data in GigaDB here: http://dx.doi.org/10.5524/100051

Now known as DNBSEQ-G50

See Parasite Award website here: https://researchparasite.com/

See the NCBI short read archive (SRA) and Gene Expression Omnibus (GEO) databases here:

https://www.ncbi.nlm.nih.gov/sra/ https://www.ncbi.nlm.nih.gov/geo/

Other centralized data repositories are available.

Read more about eLife's reproducible document stack here https://elifesciences.org/labs/b521cf4d/reproducible-document-stack-towards-a-scalable-solution-for-reproducible-articles

We wrote about our first experiences publishing virtual machines back in 2014 http://gigasciencejournal.com/blog/publishing-our-first-virtual-box-of-delights-to-aid-the-fight-against-heart-disease/

GigaScience has hypothes.is integration, and you can read more about how we are using it to add value to papers in this GigaBlog posting http://gigasciencejournal.com/blog/hypothes-is-integration/

Another example is the Bauhinia Genome project that has used the crowdfunded genomics data to educated the public and teach MSc students at the Chinese University of Hong Kong genome assembly http://bauhiniagenome.hk/2018/03/crowdfunded-genomes-and-the-plant-genome-big-bang/

There have even been community funded genome projects such as the "peoples parrot" and Azolla genome project, with strong education components such as this one (although using short reads to make an initial draft genome) http://gigasciencejournal.com/blog/community-genomes-from-the-peoples-parrot-to-crowdfernding/

Pig gut dataset in GigaDB http://dx.doi.org/10.5524/100187

Like this data many hosted in our GigaDB repository, and this has been covered in more detail in GigaBlog http://gigasciencejournal.com/blog/monkey-microbiome/

All the remaining penguin species have now also been sequenced in a follow-up study, see https://doi.org/10.1093/gigascience/giz117

This URL doesn't work any more but the DOI redirects it to the new location https://doi.org/10.1186/2047-217X-3-27

Coverage of this here https://nationalmuseumpublications.co.za/making-the-untouchable-touchable/

See museum website here https://nasmus.co.za/

Eventually published in GigaDB http://dx.doi.org/10.5524/100627

Inspiring the film "The Birds", which you can read more in the Sanger Institute blog https://sangerinstitute.blog/2020/05/04/prising-open-the-scallop-genome/

This Q&A features some discussion of her contribution to this project

This project's goal is to sequence 25 novel genomes representing UK biodiversity, as part of the Wellcome Sanger Institute's wider 25th Anniversary celebrations. See https://www.sanger.ac.uk/science/collaboration/25-genomes-25-years

Also known as the flame jellyfish https://en.wikipedia.org/wiki/Rhopilema_esculentum

We've published and written more on some of these genomes here: http://gigasciencejournal.com/blog/jellyfish-genomes/

In Tibet this type of yak-cow hybrid is know as a "dzo" (མཛོ)་ https://en.wikipedia.org/wiki/Dzo

See the Q&A with Benjamin Rosen and Timothy Smith in GigaBlog for more insight http://gigasciencejournal.com/blog/dna-day-2020-cattle-reference-genome/

See the Q&A with Benjamin Rosen & Timothy Smith in GigaBlog for more insight into this work http://gigasciencejournal.com/blog/dna-day-2020-cattle-reference-genome/

NPR has covered this famous cow https://www.npr.org/templates/story/story.php?storyId=103382511

Including COVID-19, as it is estimated 50% of patients with COVID-19 who have died had secondary bacterial infections. Watch the COSMIC project looking at metagenomics of respiratory samples to identify the bacteria, fungi, and viral co-infections present in patients with COVID-19 https://www.covid-coinfections.org/t/cosmic-co-infections-and-secondary-microbial-infections-in-covid-19/17

See also a Chinese language adaptation of this statement in Bull. Ntnl. Nat. Sci Foundation China. http://www.cnki.net/kcms/doi/10.16262/j.cnki.1000-8217.2018.06.001.html

See also a Chinese language adaptation of this statement in Bull. Ntnl. Nat. Sci Foundation China. http://www.cnki.net/kcms/doi/10.16262/j.cnki.1000-8217.2018.06.001.html

A more detailed version of this clarification and background is available via our blog: http://gigasciencejournal.com/blog/appropriate-authorship/

‡ Senior author

This was a winner of the 2018 GigaScience prize and presented at the ICG13 conference in Shenzhen. See video here https://youtu.be/7W6EDZhnvb4

A Keynote on Open Humans was presented by author Madeline Ball at BOSC (Bioinformatics Open Source Conference) and is viewable here https://youtu.be/CegpG10VPvM

You can watch a video presentation of this work recorded at the Galaxy Community Conference from author Nicola Soranzo here https://vimeo.com/296964100

More on Nala in the Vet Candy blog https://www.myvetcandy.com/clinicalupdblog/2020/4/2/first-complete-german-shepherd-dna-offers-new-tool-to-fight-disease

Coverage in GenomeWeb https://www.genomeweb.com/scan/german-shepherds-own-sequence#.XoeoXG4o-qA

See the homepage for updates taking it towards PLINO 2.0 alpha https://www.cog-genomics.org/plink/2.0/

We also have phased and annotated data for use in plink2.0 worked examples in GigaDB http://dx.doi.org/10.5524/100516

A peer reviewed and updated version of this has now been published in GigaScience https://doi.org/10.1093/gigascience/giaa004

Some of the authors have recorded a podcast discussing the implications for algae research from this data https://podcasts.apple.com/us/podcast/gane-ka-shu-wong-michael-melkonian-on-if-algae-can/id1420197433?i=1000458893924

GigaScience carry out Open Peer review and you can read the peer reviews via these DOIs:

Joon-Ho Yu: http://dx.doi.org/10.5524/REVIEW.101788 Birgit Wouters: http://dx.doi.org/10.5524/REVIEW.101787

This has been recommended and reviewed by F1000 https://f1000.com/prime/731984614

This has been recommended and reviewed by F1000 https://f1000.com/prime/734961664

This has been recommended and reviewed by F1000 here https://f1000.com/prime/735958664

This has been highlighted and reviewed by F1000 https://f1000.com/prime/718180400

Please add comments directly on the key parts of the commentary you would like to raise any issues with.

Some examples of forensic entomology highlighted here https://www.wired.com/2013/10/when-crime-scene-evidence-crawls-away/

30 leading publishers have all made their coronavirus related content open access in this manner https://wellcome.ac.uk/press-release/publishers-make-coronavirus-covid-19-content-freely-available-and-reusable

This follows on from previous infectious disease modelling guest blogs from Dr Mike Dean on Ebola http://gigasciencejournal.com/blog/guest-blog-the-2014-ebola-epidemic-approaches-and-resources-to-slow-the-spread-of-infection/ and Zika http://gigasciencejournal.com/blog/guest-blog-mind-zika-data-gap/

Using hypothes.is this information can also be updated via annotations here. e.g. adding mention of Twist biosciences, whose Oligo pools are utilized in many CRISPR applications including generation of CRISPR guide RNA (sgRNA) libraries. See https://www.twistbioscience.com/products/oligopools

Given that new methods, kits, and services continue to be rapidly developed and updated, an editable version we set up on Github wiki, and readers encourage to update it. See https://github.com/gigascience/paper-chen2014/wiki

See some media coverage of this work here https://news.cgtn.com/news/2020-03-24/Scientists-release-genome-of-agarwood-tree-Aquilaria-sinensis-P7q0PlxXmo/index.html

Despite being the reason Hong Kong was known as the "fragrant harbour" these tree's are heavily poached and nearly extinct in the wild in Hong Kong http://www.bbc.com/travel/story/20170306-the-scent-thats-pricier-than-gold

Even without reference genomes, mining metagenomes for coronavirus sequences has become particularly topical in 2020. See the Pangolin 2019-nCoV-like coronavirus example https://doi.org/10.1101/2020.02.08.939660

Jennifer Gardy discusses the groundbreaking H1N1 crowdsourcing efforts in her TEDx talk here (with lots of lessons for the coronavirus outbreak a decade later) https://www.youtube.com/watch?v=LmAugMSJ1-Y

See more in GigaBlog about the novel "tweenome" method of datasharing for this project http://gigasciencejournal.com/blog/notes-from-an-e-coli-tweenome-lessons-learned-from-our-first-data-doi/

Mining metagenomes for coronavirus sequences has become particularly topical in 2020 (see the Pangolin 2019-nCoV-like coronavirus example https://doi.org/10.1101/2020.02.08.939660)

As this works with RNA viruses it has been made part of the "Free access to OUP resources on coronavirus and related topics" collection on the Oxford University Press website https://academic.oup.com/journals/pages/coronavirus

This approach of using Oxford Nanopore direct-RNA sequencing for viruses has now been carried out on the SARSCov2/COVID19 causing coronavirus. See https://doi.org/10.1101/2020.03.05.976167

This galaxy + viral genome assembly approach has been updated in 2020 to analyze and store COVID19/SARSCov2 data https://covid19.galaxyproject.org/

Taylor Noble video abstract: https://youtu.be/NQjmxE4Frxo

One of the authors has presented a talk on the Citizen Science offshoot of this project here https://youtu.be/t6WpLbd0Nf8

See the CAMI website https://data.cami-challenge.org/

The Fort Lauderdale agreement followed these up in 2003, but there has been a long gap since then https://www.genome.gov/10506537/reaffirmation-and-extension-of-nhgri-rapid-data-release-policies

And it has just been reported in Connecticut https://www.nbcconnecticut.com/news/local/Destructive-Spotted-Lanternfly-Spotted-in-Connecticut-563208361.html

See the press release here discussing the novelty of this data https://www.eurekalert.org/pub_releases/2019-10/udoa-fgo101619.php

Data in GigaDB here: http://dx.doi.org/10.5524/102171

See https://www.ncbi.nlm.nih.gov/genome/?term=Saccharomyces%20cerevisiae[Organism]&cmd=DetailsSearch

Also know as the scarlet eggplant or bitter tomato.

The African eggplant is a good example of the work of the Africa Orphan Crop consortium and many of the authors are consortium members. You can read more on the first genomes released in GigaBlog here: http://gigasciencejournal.com/blog/democratising-data-aocc/