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MRG: upd citations, minor text #3220

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MRG: upd citations, minor text #3220

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upd citations, minor text
bluegenes Jun 19, 2024
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bluegenes Jun 20, 2024
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bluegenes Jun 20, 2024
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11 changes: 6 additions & 5 deletions paper.bib
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Expand Up @@ -78,12 +78,13 @@ @article{hera2023deriving
publisher={Cold Spring Harbor Lab}
}

@article{liu2023fast,
doi={10.1101/2023.11.06.565843},
url={https://doi.org/10.1101/2023.11.06.565843},
@article{hera2023fast,
title={Fast, lightweight, and accurate metagenomic functional profiling using FracMinHash sketches},
author={Liu, S and Wei, W and Ma, C and Koslicki, D and others},
year={2023}
author={Rahman Hera, Mahmudur and Liu, Shaopeng and Wei, Wei and Rodriguez, Judith S and Ma, Chunyu and Koslicki, David},
journal={bioRxiv},
pages={2023--11},
year={2023},
publisher={Cold Spring Harbor Laboratory}
}

@article{portik2022evaluation,
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6 changes: 3 additions & 3 deletions paper.md
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Expand Up @@ -129,7 +129,7 @@ of DNA, RNA, and amino acid k-mers for biological sequence search, comparison,
and analysis [@Pierce:2019]. sourmash's FracMinHash sketching supports fast and
accurate sequence comparisons between datasets of different sizes [@gather],
including taxonomic profiling [@portik2022evaluation], functional profiling
[@liu2023fast], and petabase-scale sequence search [@branchwater]. From
[@hera2023fast], and petabase-scale sequence search [@branchwater]. From
release 4.x, sourmash is built on top of Rust and provides an experimental
Rust interface.

Expand All @@ -150,14 +150,14 @@ and Containment calculations, which enables analysis and comparison of data
sets of different sizes, including large metagenomic samples. As of v4.4,
sourmash can convert these to estimated Average Nucleotide Identity (ANI)
values, which can provide improved biological context to sketch comparisons
[@hera2022debiasing].
[@hera2023deriving].

# Statement of Need

Large collections of genomes, transcriptomes, and raw sequencing data sets are
readily available in biology, and the field needs lightweight computational
methods for searching and summarizing the content of both public and private
collections. sourmash provides a flexible set of programmatic functionality
collections. sourmash provides a flexible set of programmatic tools
for this purpose, together with a robust and well-tested command-line
interface. It has been used in over 350 publications (based on citations of
@Brown:2016 and @Pierce:2019) and it continues to expand in functionality.
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