-
Notifications
You must be signed in to change notification settings - Fork 21
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #5902 from openjournals/joss.07066
Merging automatically
- Loading branch information
Showing
3 changed files
with
1,165 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,374 @@ | ||
<?xml version="1.0" encoding="UTF-8"?> | ||
<doi_batch xmlns="http://www.crossref.org/schema/5.3.1" | ||
xmlns:ai="http://www.crossref.org/AccessIndicators.xsd" | ||
xmlns:rel="http://www.crossref.org/relations.xsd" | ||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" | ||
version="5.3.1" | ||
xsi:schemaLocation="http://www.crossref.org/schema/5.3.1 http://www.crossref.org/schemas/crossref5.3.1.xsd"> | ||
<head> | ||
<doi_batch_id>20240923141827-fc7018f9906a3d6fee441efb30ecb4ad06627af0</doi_batch_id> | ||
<timestamp>20240923141827</timestamp> | ||
<depositor> | ||
<depositor_name>JOSS Admin</depositor_name> | ||
<email_address>[email protected]</email_address> | ||
</depositor> | ||
<registrant>The Open Journal</registrant> | ||
</head> | ||
<body> | ||
<journal> | ||
<journal_metadata> | ||
<full_title>Journal of Open Source Software</full_title> | ||
<abbrev_title>JOSS</abbrev_title> | ||
<issn media_type="electronic">2475-9066</issn> | ||
<doi_data> | ||
<doi>10.21105/joss</doi> | ||
<resource>https://joss.theoj.org</resource> | ||
</doi_data> | ||
</journal_metadata> | ||
<journal_issue> | ||
<publication_date media_type="online"> | ||
<month>09</month> | ||
<year>2024</year> | ||
</publication_date> | ||
<journal_volume> | ||
<volume>9</volume> | ||
</journal_volume> | ||
<issue>101</issue> | ||
</journal_issue> | ||
<journal_article publication_type="full_text"> | ||
<titles> | ||
<title>Back to sequences: Find the origin of k-mers</title> | ||
</titles> | ||
<contributors> | ||
<person_name sequence="first" contributor_role="author"> | ||
<given_name>Anthony</given_name> | ||
<surname>Baire</surname> | ||
</person_name> | ||
<person_name sequence="additional" | ||
contributor_role="author"> | ||
<given_name>Pierre</given_name> | ||
<surname>Marijon</surname> | ||
<ORCID>https://orcid.org/0000-0002-6694-6873</ORCID> | ||
</person_name> | ||
<person_name sequence="additional" | ||
contributor_role="author"> | ||
<given_name>Francesco</given_name> | ||
<surname>Andreace</surname> | ||
<ORCID>https://orcid.org/0009-0008-0566-200X</ORCID> | ||
</person_name> | ||
<person_name sequence="additional" | ||
contributor_role="author"> | ||
<given_name>Pierre</given_name> | ||
<surname>Peterlongo</surname> | ||
<ORCID>https://orcid.org/0000-0003-0776-6407</ORCID> | ||
</person_name> | ||
</contributors> | ||
<publication_date> | ||
<month>09</month> | ||
<day>23</day> | ||
<year>2024</year> | ||
</publication_date> | ||
<pages> | ||
<first_page>7066</first_page> | ||
</pages> | ||
<publisher_item> | ||
<identifier id_type="doi">10.21105/joss.07066</identifier> | ||
</publisher_item> | ||
<ai:program name="AccessIndicators"> | ||
<ai:license_ref applies_to="vor">http://creativecommons.org/licenses/by/4.0/</ai:license_ref> | ||
<ai:license_ref applies_to="am">http://creativecommons.org/licenses/by/4.0/</ai:license_ref> | ||
<ai:license_ref applies_to="tdm">http://creativecommons.org/licenses/by/4.0/</ai:license_ref> | ||
</ai:program> | ||
<rel:program> | ||
<rel:related_item> | ||
<rel:description>Software archive</rel:description> | ||
<rel:inter_work_relation relationship-type="references" identifier-type="doi">10.5281/zenodo.13794732</rel:inter_work_relation> | ||
</rel:related_item> | ||
<rel:related_item> | ||
<rel:description>GitHub review issue</rel:description> | ||
<rel:inter_work_relation relationship-type="hasReview" identifier-type="uri">https://github.com/openjournals/joss-reviews/issues/7066</rel:inter_work_relation> | ||
</rel:related_item> | ||
</rel:program> | ||
<doi_data> | ||
<doi>10.21105/joss.07066</doi> | ||
<resource>https://joss.theoj.org/papers/10.21105/joss.07066</resource> | ||
<collection property="text-mining"> | ||
<item> | ||
<resource mime_type="application/pdf">https://joss.theoj.org/papers/10.21105/joss.07066.pdf</resource> | ||
</item> | ||
</collection> | ||
</doi_data> | ||
<citation_list> | ||
<citation key="pt"> | ||
<article_title>The Platinum Searcher</article_title> | ||
<author>Monochromegane</author> | ||
<cYear>2018</cYear> | ||
<unstructured_citation>Monochromegane. (2018). The Platinum | ||
Searcher. | ||
https://github.com/monochromegane/the_platinum_searcher.</unstructured_citation> | ||
</citation> | ||
<citation key="ag"> | ||
<article_title>The Silver Searcher</article_title> | ||
<author>Greer</author> | ||
<cYear>2020</cYear> | ||
<unstructured_citation>Greer, G. (2020). The Silver | ||
Searcher. | ||
https://github.com/ggreer/the_silver_searcher.</unstructured_citation> | ||
</citation> | ||
<citation key="kmermapper"> | ||
<article_title>Kmer Mapper</article_title> | ||
<author>Ivar Grytten</author> | ||
<cYear>2020</cYear> | ||
<unstructured_citation>Ivar Grytten, K. D. R. (2020). Kmer | ||
Mapper. https://github.com/ivargr/kmer_mapper.</unstructured_citation> | ||
</citation> | ||
<citation key="grytten2022kage"> | ||
<article_title>KAGE: Fast alignment-free graph-based | ||
genotyping of SNPs and short indels</article_title> | ||
<author>Grytten</author> | ||
<journal_title>Genome Biology</journal_title> | ||
<issue>1</issue> | ||
<volume>23</volume> | ||
<doi>10.1186/s13059-022-02771-2</doi> | ||
<cYear>2022</cYear> | ||
<unstructured_citation>Grytten, I., Dagestad Rand, K., & | ||
Sandve, G. K. (2022). KAGE: Fast alignment-free graph-based genotyping | ||
of SNPs and short indels. Genome Biology, 23(1), 209. | ||
https://doi.org/10.1186/s13059-022-02771-2</unstructured_citation> | ||
</citation> | ||
<citation key="flicek2009sense"> | ||
<article_title>Sense from sequence reads: Methods for | ||
alignment and assembly</article_title> | ||
<author>Flicek</author> | ||
<journal_title>Nature methods</journal_title> | ||
<issue>Suppl 11</issue> | ||
<volume>6</volume> | ||
<doi>10.1038/nmeth.1376</doi> | ||
<cYear>2009</cYear> | ||
<unstructured_citation>Flicek, P., & Birney, E. (2009). | ||
Sense from sequence reads: Methods for alignment and assembly. Nature | ||
Methods, 6(Suppl 11), S6–S12. | ||
https://doi.org/10.1038/nmeth.1376</unstructured_citation> | ||
</citation> | ||
<citation key="schatz2010assembly"> | ||
<article_title>Assembly of large genomes using | ||
second-generation sequencing</article_title> | ||
<author>Schatz</author> | ||
<journal_title>Genome research</journal_title> | ||
<issue>9</issue> | ||
<volume>20</volume> | ||
<doi>10.1101/gr.101360.109</doi> | ||
<cYear>2010</cYear> | ||
<unstructured_citation>Schatz, M. C., Delcher, A. L., & | ||
Salzberg, S. L. (2010). Assembly of large genomes using | ||
second-generation sequencing. Genome Research, 20(9), 1165–1173. | ||
https://doi.org/10.1101/gr.101360.109</unstructured_citation> | ||
</citation> | ||
<citation key="benoit2016multiple"> | ||
<article_title>Multiple comparative metagenomics using | ||
multiset k-mer counting</article_title> | ||
<author>Benoit</author> | ||
<journal_title>PeerJ Computer Science</journal_title> | ||
<volume>2</volume> | ||
<doi>10.7717/peerj-cs.94</doi> | ||
<cYear>2016</cYear> | ||
<unstructured_citation>Benoit, G., Peterlongo, P., | ||
Mariadassou, M., Drezen, E., Schbath, S., Lavenier, D., & Lemaitre, | ||
C. (2016). Multiple comparative metagenomics using multiset k-mer | ||
counting. PeerJ Computer Science, 2, e94. | ||
https://doi.org/10.7717/peerj-cs.94</unstructured_citation> | ||
</citation> | ||
<citation key="li2012comparison"> | ||
<article_title>Comparison of the two major classes of | ||
assembly algorithms: Overlap–layout–consensus and | ||
de-bruijn-graph</article_title> | ||
<author>Li</author> | ||
<journal_title>Briefings in functional | ||
genomics</journal_title> | ||
<issue>1</issue> | ||
<volume>11</volume> | ||
<doi>10.1093/bfgp/elr035</doi> | ||
<cYear>2012</cYear> | ||
<unstructured_citation>Li, Z., Chen, Y., Mu, D., Yuan, J., | ||
Shi, Y., Zhang, H., Gan, J., Li, N., Hu, X., Liu, B., & others. | ||
(2012). Comparison of the two major classes of assembly algorithms: | ||
Overlap–layout–consensus and de-bruijn-graph. Briefings in Functional | ||
Genomics, 11(1), 25–37. | ||
https://doi.org/10.1093/bfgp/elr035</unstructured_citation> | ||
</citation> | ||
<citation key="sarmashghi2019skmer"> | ||
<article_title>Skmer: Assembly-free and alignment-free | ||
sample identification using genome skims</article_title> | ||
<author>Sarmashghi</author> | ||
<journal_title>Genome biology</journal_title> | ||
<volume>20</volume> | ||
<doi>10.1186/s13059-019-1632-4</doi> | ||
<cYear>2019</cYear> | ||
<unstructured_citation>Sarmashghi, S., Bohmann, K., P. | ||
Gilbert, M. T., Bafna, V., & Mirarab, S. (2019). Skmer: | ||
Assembly-free and alignment-free sample identification using genome | ||
skims. Genome Biology, 20, 1–20. | ||
https://doi.org/10.1186/s13059-019-1632-4</unstructured_citation> | ||
</citation> | ||
<citation key="zhang2014rna"> | ||
<article_title>RNA-skim: A rapid method for RNA-seq | ||
quantification at transcript level</article_title> | ||
<author>Zhang</author> | ||
<journal_title>Bioinformatics</journal_title> | ||
<issue>12</issue> | ||
<volume>30</volume> | ||
<doi>10.1093/bioinformatics/btu288</doi> | ||
<cYear>2014</cYear> | ||
<unstructured_citation>Zhang, Z., & Wang, W. (2014). | ||
RNA-skim: A rapid method for RNA-seq quantification at transcript level. | ||
Bioinformatics, 30(12), i283–i292. | ||
https://doi.org/10.1093/bioinformatics/btu288</unstructured_citation> | ||
</citation> | ||
<citation key="uricaru2015reference"> | ||
<article_title>Reference-free detection of isolated | ||
SNPs</article_title> | ||
<author>Uricaru</author> | ||
<journal_title>Nucleic acids research</journal_title> | ||
<issue>2</issue> | ||
<volume>43</volume> | ||
<doi>10.1093/nar/gku1187</doi> | ||
<cYear>2015</cYear> | ||
<unstructured_citation>Uricaru, R., Rizk, G., Lacroix, V., | ||
Quillery, E., Plantard, O., Chikhi, R., Lemaitre, C., & Peterlongo, | ||
P. (2015). Reference-free detection of isolated SNPs. Nucleic Acids | ||
Research, 43(2), e11–e11. | ||
https://doi.org/10.1093/nar/gku1187</unstructured_citation> | ||
</citation> | ||
<citation key="lemane2022kmtricks"> | ||
<article_title>Kmtricks: Efficient and flexible construction | ||
of bloom filters for large sequencing data collections</article_title> | ||
<author>Lemane</author> | ||
<journal_title>Bioinformatics Advances</journal_title> | ||
<issue>1</issue> | ||
<volume>2</volume> | ||
<doi>10.1093/bioadv/vbac029</doi> | ||
<cYear>2022</cYear> | ||
<unstructured_citation>Lemane, T., Medvedev, P., Chikhi, R., | ||
& Peterlongo, P. (2022). Kmtricks: Efficient and flexible | ||
construction of bloom filters for large sequencing data collections. | ||
Bioinformatics Advances, 2(1), vbac029. | ||
https://doi.org/10.1093/bioadv/vbac029</unstructured_citation> | ||
</citation> | ||
<citation key="cracco2023extremely"> | ||
<article_title>Extremely fast construction and querying of | ||
compacted and colored de bruijn graphs with GGCAT</article_title> | ||
<author>Cracco</author> | ||
<journal_title>Genome Research</journal_title> | ||
<doi>10.1101/gr.277615.122</doi> | ||
<cYear>2023</cYear> | ||
<unstructured_citation>Cracco, A., & Tomescu, A. I. | ||
(2023). Extremely fast construction and querying of compacted and | ||
colored de bruijn graphs with GGCAT. Genome Research, gr–277615. | ||
https://doi.org/10.1101/gr.277615.122</unstructured_citation> | ||
</citation> | ||
<citation key="huson2002greedy"> | ||
<article_title>The greedy path-merging algorithm for contig | ||
scaffolding</article_title> | ||
<author>Huson</author> | ||
<journal_title>Journal of the ACM (JACM)</journal_title> | ||
<issue>5</issue> | ||
<volume>49</volume> | ||
<doi>10.1145/585265.585267</doi> | ||
<cYear>2002</cYear> | ||
<unstructured_citation>Huson, D. H., Reinert, K., & | ||
Myers, E. W. (2002). The greedy path-merging algorithm for contig | ||
scaffolding. Journal of the ACM (JACM), 49(5), 603–615. | ||
https://doi.org/10.1145/585265.585267</unstructured_citation> | ||
</citation> | ||
<citation key="bankevich2012spades"> | ||
<article_title>SPAdes: A new genome assembly algorithm and | ||
its applications to single-cell sequencing</article_title> | ||
<author>Bankevich</author> | ||
<journal_title>Journal of computational | ||
biology</journal_title> | ||
<issue>5</issue> | ||
<volume>19</volume> | ||
<doi>10.1089/cmb.2012.0021</doi> | ||
<cYear>2012</cYear> | ||
<unstructured_citation>Bankevich, A., Nurk, S., Antipov, D., | ||
Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, | ||
S. I., Pham, S., Prjibelski, A. D., & others. (2012). SPAdes: A new | ||
genome assembly algorithm and its applications to single-cell | ||
sequencing. Journal of Computational Biology, 19(5), 455–477. | ||
https://doi.org/10.1089/cmb.2012.0021</unstructured_citation> | ||
</citation> | ||
<citation key="marchet2020resource"> | ||
<article_title>A resource-frugal probabilistic dictionary | ||
and applications in bioinformatics</article_title> | ||
<author>Marchet</author> | ||
<journal_title>Discrete Applied Mathematics</journal_title> | ||
<volume>274</volume> | ||
<doi>10.1016/j.dam.2018.03.035</doi> | ||
<cYear>2020</cYear> | ||
<unstructured_citation>Marchet, C., Lecompte, L., Limasset, | ||
A., Bittner, L., & Peterlongo, P. (2020). A resource-frugal | ||
probabilistic dictionary and applications in bioinformatics. Discrete | ||
Applied Mathematics, 274, 92–102. | ||
https://doi.org/10.1016/j.dam.2018.03.035</unstructured_citation> | ||
</citation> | ||
<citation key="wood2019improved"> | ||
<article_title>Improved metagenomic analysis with kraken | ||
2</article_title> | ||
<author>Wood</author> | ||
<journal_title>Genome biology</journal_title> | ||
<volume>20</volume> | ||
<doi>10.1186/s13059-019-1891-0</doi> | ||
<cYear>2019</cYear> | ||
<unstructured_citation>Wood, D. E., Lu, J., & Langmead, | ||
B. (2019). Improved metagenomic analysis with kraken 2. Genome Biology, | ||
20, 1–13. | ||
https://doi.org/10.1186/s13059-019-1891-0</unstructured_citation> | ||
</citation> | ||
<citation key="lemane2022k"> | ||
<article_title>Kmdiff, large-scale and user-friendly | ||
differential k-mer analyses</article_title> | ||
<author>Lemane</author> | ||
<journal_title>Bioinformatics</journal_title> | ||
<issue>24</issue> | ||
<volume>38</volume> | ||
<doi>10.1093/bioinformatics/btac689</doi> | ||
<cYear>2022</cYear> | ||
<unstructured_citation>Lemane, T., Chikhi, R., & | ||
Peterlongo, P. (2022). Kmdiff, large-scale and user-friendly | ||
differential k-mer analyses. Bioinformatics, 38(24), 5443–5445. | ||
https://doi.org/10.1093/bioinformatics/btac689</unstructured_citation> | ||
</citation> | ||
<citation key="plaza2015quality"> | ||
<article_title>Quality control of microbiota metagenomics by | ||
k-mer analysis</article_title> | ||
<author>Plaza Onate</author> | ||
<journal_title>BMC genomics</journal_title> | ||
<volume>16</volume> | ||
<doi>10.1186/s12864-015-1406-7</doi> | ||
<cYear>2015</cYear> | ||
<unstructured_citation>Plaza Onate, F., Batto, J.-M., Juste, | ||
C., Fadlallah, J., Fougeroux, C., Gouas, D., Pons, N., Kennedy, S., | ||
Levenez, F., Dore, J., & others. (2015). Quality control of | ||
microbiota metagenomics by k-mer analysis. BMC Genomics, 16, 1–10. | ||
https://doi.org/10.1186/s12864-015-1406-7</unstructured_citation> | ||
</citation> | ||
<citation key="gonzalez2023akmerbroom"> | ||
<article_title>aKmerBroom: Ancient oral DNA decontamination | ||
using bloom filters on k-mer sets</article_title> | ||
<author>González</author> | ||
<journal_title>Iscience</journal_title> | ||
<issue>11</issue> | ||
<volume>26</volume> | ||
<doi>10.1016/j.isci.2023.108057</doi> | ||
<cYear>2023</cYear> | ||
<unstructured_citation>González, C. D., Rangavittal, S., | ||
Vicedomini, R., Chikhi, R., & Richard, H. (2023). aKmerBroom: | ||
Ancient oral DNA decontamination using bloom filters on k-mer sets. | ||
Iscience, 26(11). | ||
https://doi.org/10.1016/j.isci.2023.108057</unstructured_citation> | ||
</citation> | ||
</citation_list> | ||
</journal_article> | ||
</journal> | ||
</body> | ||
</doi_batch> |
Binary file not shown.
Oops, something went wrong.