Skip to content

Commit e9cecec

Browse files
editorialboteditorialbot
authored
Merge pull request #6902 from openjournals/joss.08048
Merging automatically
2 parents 2da131e + 9229bf6 commit e9cecec

File tree

3 files changed

+776
-0
lines changed

3 files changed

+776
-0
lines changed

‎joss.08048/10.21105.joss.08048.crossref.xml

Lines changed: 217 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,217 @@
1+
<?xml version="1.0" encoding="UTF-8"?>
2+
<doi_batch xmlns="http://www.crossref.org/schema/5.3.1"
3+
xmlns:ai="http://www.crossref.org/AccessIndicators.xsd"
4+
xmlns:rel="http://www.crossref.org/relations.xsd"
5+
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
6+
version="5.3.1"
7+
xsi:schemaLocation="http://www.crossref.org/schema/5.3.1 http://www.crossref.org/schemas/crossref5.3.1.xsd">
8+
<head>
9+
<doi_batch_id>20250630114259-ad42f2e36ea148ab31beac0d780704086315c70b</doi_batch_id>
10+
<timestamp>20250630114259</timestamp>
11+
<depositor>
12+
<depositor_name>JOSS Admin</depositor_name>
13+
<email_address>[email protected]</email_address>
14+
</depositor>
15+
<registrant>The Open Journal</registrant>
16+
</head>
17+
<body>
18+
<journal>
19+
<journal_metadata>
20+
<full_title>Journal of Open Source Software</full_title>
21+
<abbrev_title>JOSS</abbrev_title>
22+
<issn media_type="electronic">2475-9066</issn>
23+
<doi_data>
24+
<doi>10.21105/joss</doi>
25+
<resource>https://joss.theoj.org</resource>
26+
</doi_data>
27+
</journal_metadata>
28+
<journal_issue>
29+
<publication_date media_type="online">
30+
<month>06</month>
31+
<year>2025</year>
32+
</publication_date>
33+
<journal_volume>
34+
<volume>10</volume>
35+
</journal_volume>
36+
<issue>110</issue>
37+
</journal_issue>
38+
<journal_article publication_type="full_text">
39+
<titles>
40+
<title>grepq: A Rust application that quickly filters FASTQ files by matching sequences to a set of regular expressions</title>
41+
</titles>
42+
<contributors>
43+
<person_name sequence="first" contributor_role="author">
44+
<given_name>Nicholas D.</given_name>
45+
<surname>Crosbie</surname>
46+
<affiliations>
47+
<institution><institution_name>Melbourne Veterinary School, University of Melbourne, Parkville, Victoria, Australia</institution_name></institution>
48+
</affiliations>
49+
<ORCID>https://orcid.org/0000-0002-0319-4248</ORCID>
50+
</person_name>
51+
</contributors>
52+
<publication_date>
53+
<month>06</month>
54+
<day>30</day>
55+
<year>2025</year>
56+
</publication_date>
57+
<pages>
58+
<first_page>8048</first_page>
59+
</pages>
60+
<publisher_item>
61+
<identifier id_type="doi">10.21105/joss.08048</identifier>
62+
</publisher_item>
63+
<ai:program name="AccessIndicators">
64+
<ai:license_ref applies_to="vor">http://creativecommons.org/licenses/by/4.0/</ai:license_ref>
65+
<ai:license_ref applies_to="am">http://creativecommons.org/licenses/by/4.0/</ai:license_ref>
66+
<ai:license_ref applies_to="tdm">http://creativecommons.org/licenses/by/4.0/</ai:license_ref>
67+
</ai:program>
68+
<rel:program>
69+
<rel:related_item>
70+
<rel:description>Software archive</rel:description>
71+
<rel:inter_work_relation relationship-type="references" identifier-type="doi">10.5281/zenodo.15612061</rel:inter_work_relation>
72+
</rel:related_item>
73+
<rel:related_item>
74+
<rel:description>GitHub review issue</rel:description>
75+
<rel:inter_work_relation relationship-type="hasReview" identifier-type="uri">https://github.com/openjournals/joss-reviews/issues/8048</rel:inter_work_relation>
76+
</rel:related_item>
77+
</rel:program>
78+
<doi_data>
79+
<doi>10.21105/joss.08048</doi>
80+
<resource>https://joss.theoj.org/papers/10.21105/joss.08048</resource>
81+
<collection property="text-mining">
82+
<item>
83+
<resource mime_type="application/pdf">https://joss.theoj.org/papers/10.21105/joss.08048.pdf</resource>
84+
</item>
85+
</collection>
86+
</doi_data>
87+
<citation_list>
88+
<citation key="kleene1951representationof">
89+
<article_title>Representationof events in nerve nets and finite automata</article_title>
90+
<author>Kleene</author>
91+
<journal_title>CE Shannon and J. McCarthy</journal_title>
92+
<doi>10.1515/9781400882618-002</doi>
93+
<cYear>1951</cYear>
94+
<unstructured_citation>Kleene, S. (1951). Representationof events in nerve nets and finite automata. CE Shannon and J. McCarthy. https://doi.org/10.1515/9781400882618-002</unstructured_citation>
95+
</citation>
96+
<citation key="hodgman2000historical">
97+
<article_title>A historical perspective on gene/protein functional assignment</article_title>
98+
<author>Hodgman</author>
99+
<journal_title>Bioinformatics</journal_title>
100+
<issue>1</issue>
101+
<volume>16</volume>
102+
<doi>10.1093/bioinformatics/16.1.10</doi>
103+
<cYear>2000</cYear>
104+
<unstructured_citation>Hodgman, T. C. (2000). A historical perspective on gene/protein functional assignment. Bioinformatics, 16(1), 10–15. https://doi.org/10.1093/bioinformatics/16.1.10</unstructured_citation>
105+
</citation>
106+
<citation key="bachurin2024structural">
107+
<article_title>Structural peculiarities of tandem repeats and their clinical significance</article_title>
108+
<author>Bachurin</author>
109+
<journal_title>Biochemical and Biophysical Research Communications</journal_title>
110+
<volume>692</volume>
111+
<doi>10.1016/j.bbrc.2023.149349</doi>
112+
<cYear>2024</cYear>
113+
<unstructured_citation>Bachurin, S. S., Yurushkin, M. V., Slynko, I. A., Kletskii, M. E., Burov, O. N., &amp; Berezovskiy, D. P. (2024). Structural peculiarities of tandem repeats and their clinical significance. Biochemical and Biophysical Research Communications, 692, 149349. https://doi.org/10.1016/j.bbrc.2023.149349</unstructured_citation>
114+
</citation>
115+
<citation key="valdivia2012biodefense">
116+
<article_title>Biodefense oriented genomic-based pathogen classification systems: Challenges and opportunities</article_title>
117+
<author>Valdivia-Granda</author>
118+
<journal_title>Journal of bioterrorism &amp; biodefense</journal_title>
119+
<issue>1</issue>
120+
<volume>3</volume>
121+
<doi>10.4172/2157-2526.1000113</doi>
122+
<cYear>2012</cYear>
123+
<unstructured_citation>Valdivia-Granda, W. A. (2012). Biodefense oriented genomic-based pathogen classification systems: Challenges and opportunities. Journal of Bioterrorism &amp; Biodefense, 3(1), 1000113. https://doi.org/10.4172/2157-2526.1000113</unstructured_citation>
124+
</citation>
125+
<citation key="xylogiannopoulos2021pattern">
126+
<article_title>Pattern detection in multiple genome sequences with applications: The case of all SARS-CoV-2 complete variants</article_title>
127+
<author>Xylogiannopoulos</author>
128+
<journal_title>bioRxiv</journal_title>
129+
<doi>10.1101/2021.04.14.439840</doi>
130+
<cYear>2021</cYear>
131+
<unstructured_citation>Xylogiannopoulos, K. F. (2021). Pattern detection in multiple genome sequences with applications: The case of all SARS-CoV-2 complete variants. bioRxiv, 2021–2004. https://doi.org/10.1101/2021.04.14.439840</unstructured_citation>
132+
</citation>
133+
<citation key="choi2018wastewater">
134+
<article_title>Wastewater-based epidemiology biomarkers: Past, present and future</article_title>
135+
<author>Choi</author>
136+
<journal_title>TrAC Trends in Analytical Chemistry</journal_title>
137+
<volume>105</volume>
138+
<doi>10.1016/j.trac.2018.06.004</doi>
139+
<cYear>2018</cYear>
140+
<unstructured_citation>Choi, P. M., Tscharke, B. J., Donner, E., O’Brien, J. W., Grant, S. C., Kaserzon, S. L., Mackie, R., O’Malley, E., Crosbie, N. D., Thomas, K. V., &amp; others. (2018). Wastewater-based epidemiology biomarkers: Past, present and future. TrAC Trends in Analytical Chemistry, 105, 453–469. https://doi.org/10.1016/j.trac.2018.06.004</unstructured_citation>
141+
</citation>
142+
<citation key="sims2020future">
143+
<article_title>Future perspectives of wastewater-based epidemiology: Monitoring infectious disease spread and resistance to the community level</article_title>
144+
<author>Sims</author>
145+
<journal_title>Environment international</journal_title>
146+
<volume>139</volume>
147+
<doi>10.1016/j.envint.2020.105689</doi>
148+
<cYear>2020</cYear>
149+
<unstructured_citation>Sims, N., &amp; Kasprzyk-Hordern, B. (2020). Future perspectives of wastewater-based epidemiology: Monitoring infectious disease spread and resistance to the community level. Environment International, 139, 105689. https://doi.org/10.1016/j.envint.2020.105689</unstructured_citation>
150+
</citation>
151+
<citation key="gnugrep">
152+
<volume_title>GNU grep 3.11</volume_title>
153+
<author>Free Software Foundation</author>
154+
<cYear>2023</cYear>
155+
<unstructured_citation>Free Software Foundation. (2023). GNU grep 3.11. Free Software Foundation. https://www.gnu.org/software/grep/manual/grep.html</unstructured_citation>
156+
</citation>
157+
<citation key="awk">
158+
<volume_title>The AWK programming language</volume_title>
159+
<author>Aho</author>
160+
<cYear>1988</cYear>
161+
<unstructured_citation>Aho, A. V., Kernighan, B. W., &amp; Weinberger, P. J. (1988). The AWK programming language. https://www.cs.princeton.edu/~bwk/btl.mirror/</unstructured_citation>
162+
</citation>
163+
<citation key="gawk">
164+
<volume_title>GAWK: Effective AWK programming: A user’s guide for GNU awk, for the 5.3.1</volume_title>
165+
<author>Free Software Foundation</author>
166+
<cYear>2024</cYear>
167+
<unstructured_citation>Free Software Foundation. (2024). GAWK: Effective AWK programming: A user’s guide for GNU awk, for the 5.3.1. Free Software Foundation. https://www.gnu.org/software/gawk/manual/gawk.html</unstructured_citation>
168+
</citation>
169+
<citation key="ripgrep">
170+
<article_title>Ripgrep: Recursively search the current directory for lines matching a pattern</article_title>
171+
<author>Gallant</author>
172+
<cYear>2025</cYear>
173+
<unstructured_citation>Gallant, A. (2025). Ripgrep: Recursively search the current directory for lines matching a pattern (Version 14.1.1). https://github.com/BurntSushi/ripgrep</unstructured_citation>
174+
</citation>
175+
<citation key="seq_io">
176+
<article_title>seq_io: FASTA and FASTQ parsing and writing in Rust</article_title>
177+
<author>Schlegel</author>
178+
<cYear>2025</cYear>
179+
<unstructured_citation>Schlegel, M., &amp; Seyboldt, A. (2025). seq_io: FASTA and FASTQ parsing and writing in Rust (Version 0.3.2). https://github.com/markschl/seq_io</unstructured_citation>
180+
</citation>
181+
<citation key="regex">
182+
<article_title>regex</article_title>
183+
<author>Gallant</author>
184+
<cYear>2025</cYear>
185+
<unstructured_citation>Gallant, &amp; others. (2025). regex (Version 0.3.2). https://github.com/rust-lang/regex</unstructured_citation>
186+
</citation>
187+
<citation key="rebar">
188+
<article_title>rebar</article_title>
189+
<author>Gallant</author>
190+
<cYear>2025</cYear>
191+
<unstructured_citation>Gallant, &amp; others. (2025). rebar. https://github.com/BurntSushi/rebar</unstructured_citation>
192+
</citation>
193+
<citation key="merrett2024highly">
194+
<article_title>Highly sensitive wastewater surveillance of SARS-CoV-2 variants by targeted next-generation amplicon sequencing provides early warning of incursion in victoria, australia</article_title>
195+
<author>Merrett</author>
196+
<journal_title>Applied and Environmental Microbiology</journal_title>
197+
<issue>8</issue>
198+
<volume>90</volume>
199+
<doi>10.1128/aem.01497-23</doi>
200+
<cYear>2024</cYear>
201+
<unstructured_citation>Merrett, J. E., Nolan, M., Hartman, L., John, N., Flynn, B., Baker, L., Schang, C., McCarthy, D., Lister, D., Cheng, N. N., &amp; others. (2024). Highly sensitive wastewater surveillance of SARS-CoV-2 variants by targeted next-generation amplicon sequencing provides early warning of incursion in victoria, australia. Applied and Environmental Microbiology, 90(8), e01497–23. https://doi.org/10.1128/aem.01497-23</unstructured_citation>
202+
</citation>
203+
<citation key="katz2022sequence">
204+
<article_title>The sequence read archive: A decade more of explosive growth</article_title>
205+
<author>Katz</author>
206+
<journal_title>Nucleic acids research</journal_title>
207+
<issue>D1</issue>
208+
<volume>50</volume>
209+
<doi>10.1093/nar/gkab1053</doi>
210+
<cYear>2022</cYear>
211+
<unstructured_citation>Katz, K., Shutov, O., Lapoint, R., Kimelman, M., Brister, J. R., &amp; O’Sullivan, C. (2022). The sequence read archive: A decade more of explosive growth. Nucleic Acids Research, 50(D1), D387–D390. https://doi.org/10.1093/nar/gkab1053</unstructured_citation>
212+
</citation>
213+
</citation_list>
214+
</journal_article>
215+
</journal>
216+
</body>
217+
</doi_batch>

‎joss.08048/10.21105.joss.08048.pdf

206 KB
Binary file not shown.

0 commit comments

Comments
 (0)