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X Demographics
Mendeley readers
Attention Score in Context
| Title |
Hybrid assembly with long and short reads improves discovery of gene family expansions
|
|---|---|
| Published in |
BMC Genomics, July 2017
|
| DOI | 10.1186/s12864-017-3927-8 |
| Pubmed ID | |
| Authors |
Jason R. Miller, Peng Zhou, Joann Mudge, James Gurtowski, Hayan Lee, Thiruvarangan Ramaraj, Brian P. Walenz, Junqi Liu, Robert M. Stupar, Roxanne Denny, Li Song, Namrata Singh, Lyza G. Maron, Susan R. McCouch, W. Richard McCombie, Michael C. Schatz, Peter Tiffin, Nevin D. Young, Kevin A. T. Silverstein |
| Abstract |
Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation. We developed a hybrid assembly pipeline called "Alpaca" that can operate on 20X long-read coverage plus about 50X short-insert and 50X long-insert short-read coverage. To preclude collapse of tandem repeats, Alpaca relies on base-call-corrected long reads for contig formation. Compared to two other assembly protocols, Alpaca demonstrated the most reference agreement and repeat capture on the rice genome. On three accessions of the model legume Medicago truncatula, Alpaca generated the most agreement to a conspecific reference and predicted tandemly repeated genes absent from the other assemblies. Our results suggest Alpaca is a useful tool for investigating structural and copy number variation within de novo assemblies of sampled populations. |
X Demographics
The data shown below were collected from the profiles of 36 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 6 | 17% |
| Germany | 5 | 14% |
| Netherlands | 4 | 11% |
| Spain | 2 | 6% |
| India | 1 | 3% |
| United Kingdom | 1 | 3% |
| Canada | 1 | 3% |
| Japan | 1 | 3% |
| South Africa | 1 | 3% |
| Other | 1 | 3% |
| Unknown | 13 | 36% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 26 | 72% |
| Members of the public | 10 | 28% |
Mendeley readers
The data shown below were compiled from readership statistics for 155 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 155 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 33 | 21% |
| Student > Ph. D. Student | 29 | 19% |
| Student > Master | 24 | 15% |
| Student > Bachelor | 15 | 10% |
| Student > Doctoral Student | 7 | 5% |
| Other | 21 | 14% |
| Unknown | 26 | 17% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 54 | 35% |
| Biochemistry, Genetics and Molecular Biology | 40 | 26% |
| Computer Science | 9 | 6% |
| Environmental Science | 4 | 3% |
| Immunology and Microbiology | 3 | 2% |
| Other | 14 | 9% |
| Unknown | 31 | 20% |
Attention Score in Context
This research output has an Altmetric Attention Score of 27. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 23 October 2018.
All research outputs
#1,324,753
of 23,577,654 outputs
Outputs from BMC Genomics
#255
of 10,777 outputs
Outputs of similar age
#27,873
of 316,167 outputs
Outputs of similar age from BMC Genomics
#9
of 222 outputs
Altmetric has tracked 23,577,654 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 94th percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 10,777 research outputs from this source. They receive a mean Attention Score of 4.7. This one has done particularly well, scoring higher than 97% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 316,167 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 91% of its contemporaries.
We're also able to compare this research output to 222 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 95% of its contemporaries.