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<full_title>Journal of Open Source Software</full_title> | ||
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<citation key="ewels_multiqc_2016"> | ||
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multiple tools and samples in a single report</article_title> | ||
<author>Ewels</author> | ||
<journal_title>Bioinformatics</journal_title> | ||
<issue>19</issue> | ||
<volume>32</volume> | ||
<doi>10.1093/bioinformatics/btw354</doi> | ||
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<unstructured_citation>Ewels, P., Magnusson, M., Lundin, S., | ||
& Käller, M. (2016). MultiQC: Summarize analysis results for | ||
multiple tools and samples in a single report. Bioinformatics, 32(19), | ||
3047–3048. | ||
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<article_title>Commonalities across computational workflows | ||
for uncovering explanatory variants in undiagnosed cases</article_title> | ||
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<journal_title>Genetics in Medicine</journal_title> | ||
<issue>6</issue> | ||
<volume>23</volume> | ||
<doi>10.1038/s41436-020-01084-8</doi> | ||
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Velinder, M., Krier, J. B., LeBlanc, K., Esteves, C., Pusey, B. N., | ||
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Cogan, J., Marwaha, S., Alkelai, A., Murdock, D. R., Liu, P., Wegner, D. | ||
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<article_title>Best practices for the analytical validation | ||
of clinical whole-genome sequencing intended for the diagnosis of | ||
germline disease</article_title> | ||
<author>Marshall</author> | ||
<journal_title>npj Genomic Medicine</journal_title> | ||
<issue>1</issue> | ||
<volume>5</volume> | ||
<doi>10.1038/s41525-020-00154-9</doi> | ||
<issn>2056-7944</issn> | ||
<cYear>2020</cYear> | ||
<unstructured_citation>Marshall, C. R., Chowdhury, S., Taft, | ||
R. J., Lebo, M. S., Buchan, J. G., Harrison, S. M., Rowsey, R., Klee, E. | ||
W., Liu, P., Worthey, E. A., Jobanputra, V., Dimmock, D., Kearney, H. | ||
M., Bick, D., Kulkarni, S., Taylor, S. L., Belmont, J. W., Stavropoulos, | ||
D. J., & Lennon, N. J. (2020). Best practices for the analytical | ||
validation of clinical whole-genome sequencing intended for the | ||
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<article_title>Qualimap 2: Advanced multi-sample quality | ||
control for high-throughput sequencing data</article_title> | ||
<author>Okonechnikov</author> | ||
<journal_title>Bioinformatics</journal_title> | ||
<doi>10.1093/bioinformatics/btv566</doi> | ||
<issn>1367-4803</issn> | ||
<cYear>2015</cYear> | ||
<unstructured_citation>Okonechnikov, K., Conesa, A., & | ||
García-Alcalde, F. (2015). Qualimap 2: Advanced multi-sample quality | ||
control for high-throughput sequencing data. Bioinformatics, btv566. | ||
https://doi.org/10.1093/bioinformatics/btv566</unstructured_citation> | ||
</citation> | ||
<citation key="noauthor_picard_nodate"> | ||
<article_title>Picard toolkit</article_title> | ||
<unstructured_citation>Picard toolkit. (n.d.). Broad | ||
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<article_title>Mosdepth: Quick coverage calculation for | ||
genomes and exomes</article_title> | ||
<author>Pedersen</author> | ||
<journal_title>Bioinformatics</journal_title> | ||
<issue>5</issue> | ||
<volume>34</volume> | ||
<doi>10.1093/bioinformatics/btx699</doi> | ||
<issn>1367-4803</issn> | ||
<cYear>2018</cYear> | ||
<unstructured_citation>Pedersen, B. S., & Quinlan, A. R. | ||
(2018). Mosdepth: Quick coverage calculation for genomes and exomes. | ||
Bioinformatics, 34(5), 867–868. | ||
https://doi.org/10.1093/bioinformatics/btx699</unstructured_citation> | ||
</citation> | ||
<citation key="pedersen_indexcov_2017"> | ||
<article_title>Indexcov: Fast coverage quality control for | ||
whole-genome sequencing</article_title> | ||
<author>Pedersen</author> | ||
<journal_title>GigaScience</journal_title> | ||
<issue>11</issue> | ||
<volume>6</volume> | ||
<doi>10.1093/gigascience/gix090</doi> | ||
<issn>2047-217X</issn> | ||
<cYear>2017</cYear> | ||
<unstructured_citation>Pedersen, B. S., Collins, R. L., | ||
Talkowski, M. E., & Quinlan, A. R. (2017). Indexcov: Fast coverage | ||
quality control for whole-genome sequencing. GigaScience, 6(11). | ||
https://doi.org/10.1093/gigascience/gix090</unstructured_citation> | ||
</citation> | ||
<citation key="noauthor_covviz_nodate"> | ||
<article_title>Covviz</article_title> | ||
<unstructured_citation>Covviz. (n.d.). | ||
https://github.com/brwnj/covviz</unstructured_citation> | ||
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<citation key="danecek_twelve_2021"> | ||
<article_title>Twelve years of SAMtools and | ||
BCFtools</article_title> | ||
<author>Danecek</author> | ||
<journal_title>GigaScience</journal_title> | ||
<issue>2</issue> | ||
<volume>10</volume> | ||
<doi>10.1093/gigascience/giab008</doi> | ||
<issn>2047-217X</issn> | ||
<cYear>2021</cYear> | ||
<unstructured_citation>Danecek, P., Bonfield, J. K., Liddle, | ||
J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., | ||
McCarthy, S. A., Davies, R. M., & Li, H. (2021). Twelve years of | ||
SAMtools and BCFtools. GigaScience, 10(2), giab008. | ||
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<citation key="zhang_ancestry-agnostic_2020"> | ||
<article_title>Ancestry-agnostic estimation of DNA sample | ||
contamination from sequence reads</article_title> | ||
<author>Zhang</author> | ||
<journal_title>Genome Research</journal_title> | ||
<issue>2</issue> | ||
<volume>30</volume> | ||
<doi>10.1101/gr.246934.118</doi> | ||
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<cYear>2020</cYear> | ||
<unstructured_citation>Zhang, F., Flickinger, M., Taliun, S. | ||
A. G., InPSYght Psychiatric Genetics Consortium, Abecasis, G. R., Scott, | ||
L. J., McCaroll, S. A., Pato, C. N., Boehnke, M., & Kang, H. M. | ||
(2020). Ancestry-agnostic estimation of DNA sample contamination from | ||
sequence reads. Genome Research, 30(2), 185–194. | ||
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<citation key="pedersen_somalier_2020"> | ||
<article_title>Somalier: Rapid relatedness estimation for | ||
cancer and germline studies using efficient genome | ||
sketches</article_title> | ||
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<journal_title>Genome Medicine</journal_title> | ||
<issue>1</issue> | ||
<volume>12</volume> | ||
<doi>10.1186/s13073-020-00761-2</doi> | ||
<issn>1756-994X</issn> | ||
<cYear>2020</cYear> | ||
<unstructured_citation>Pedersen, B. S., Bhetariya, P. J., | ||
Brown, J., Kravitz, S. N., Marth, G., Jensen, R. L., Bronner, M. P., | ||
Underhill, H. R., & Quinlan, A. R. (2020). Somalier: Rapid | ||
relatedness estimation for cancer and germline studies using efficient | ||
genome sketches. Genome Medicine, 12(1), 62. | ||
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</citation> | ||
<citation key="wingett_fastq_2018"> | ||
<article_title>FastQ Screen: A tool for multi-genome mapping | ||
and quality control</article_title> | ||
<author>Wingett</author> | ||
<journal_title>F1000Research</journal_title> | ||
<volume>7</volume> | ||
<doi>10.12688/f1000research.15931.2</doi> | ||
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<unstructured_citation>Wingett, S. W., & Andrews, S. | ||
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<citation key="andrews_fastqc_2012"> | ||
<article_title>FastQC</article_title> | ||
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<unstructured_citation>Andrews, S., Krueger, F., | ||
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