2023-01-17 19:06:14 +01:00
<!DOCTYPE html>
< html xmlns = "http://www.w3.org/1999/xhtml" lang = "en" xml:lang = "en" > < head >
< meta charset = "utf-8" >
< meta name = "generator" content = "quarto-1.2.256" >
< meta name = "viewport" content = "width=device-width, initial-scale=1.0, user-scalable=yes" >
< title > OBITools V4 - References< / title >
< style >
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
div.columns{display: flex; gap: min(4vw, 1.5em);}
div.column{flex: auto; overflow-x: auto;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
ul.task-list li input[type="checkbox"] {
width: 0.8em;
margin: 0 0.8em 0.2em -1.6em;
vertical-align: middle;
}
div.csl-bib-body { }
div.csl-entry {
clear: both;
}
.hanging div.csl-entry {
margin-left:2em;
text-indent:-2em;
}
div.csl-left-margin {
min-width:2em;
float:left;
}
div.csl-right-inline {
margin-left:2em;
padding-left:1em;
}
div.csl-indent {
margin-left: 2em;
}
< / style >
< script src = "site_libs/quarto-nav/quarto-nav.js" > < / script >
< script src = "site_libs/quarto-nav/headroom.min.js" > < / script >
< script src = "site_libs/clipboard/clipboard.min.js" > < / script >
< script src = "site_libs/quarto-search/autocomplete.umd.js" > < / script >
< script src = "site_libs/quarto-search/fuse.min.js" > < / script >
< script src = "site_libs/quarto-search/quarto-search.js" > < / script >
< meta name = "quarto:offset" content = "./" >
< link href = "./annexes.html" rel = "prev" >
< script src = "site_libs/quarto-html/quarto.js" > < / script >
< script src = "site_libs/quarto-html/popper.min.js" > < / script >
< script src = "site_libs/quarto-html/tippy.umd.min.js" > < / script >
< script src = "site_libs/quarto-html/anchor.min.js" > < / script >
< link href = "site_libs/quarto-html/tippy.css" rel = "stylesheet" >
< link href = "site_libs/quarto-html/quarto-syntax-highlighting.css" rel = "stylesheet" id = "quarto-text-highlighting-styles" >
< script src = "site_libs/bootstrap/bootstrap.min.js" > < / script >
< link href = "site_libs/bootstrap/bootstrap-icons.css" rel = "stylesheet" >
< link href = "site_libs/bootstrap/bootstrap.min.css" rel = "stylesheet" id = "quarto-bootstrap" data-mode = "light" >
< script id = "quarto-search-options" type = "application/json" > {
"location": "sidebar",
"copy-button": false,
"collapse-after": 3,
"panel-placement": "start",
"type": "textbox",
"limit": 20,
"language": {
"search-no-results-text": "No results",
"search-matching-documents-text": "matching documents",
"search-copy-link-title": "Copy link to search",
"search-hide-matches-text": "Hide additional matches",
"search-more-match-text": "more match in this document",
"search-more-matches-text": "more matches in this document",
"search-clear-button-title": "Clear",
"search-detached-cancel-button-title": "Cancel",
"search-submit-button-title": "Submit"
}
}< / script >
< / head >
< body class = "nav-sidebar floating" >
< div id = "quarto-search-results" > < / div >
< header id = "quarto-header" class = "headroom fixed-top" >
< nav class = "quarto-secondary-nav" data-bs-toggle = "collapse" data-bs-target = "#quarto-sidebar" aria-controls = "quarto-sidebar" aria-expanded = "false" aria-label = "Toggle sidebar navigation" onclick = "if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }" >
< div class = "container-fluid d-flex justify-content-between" >
< h1 class = "quarto-secondary-nav-title" > References< / h1 >
< button type = "button" class = "quarto-btn-toggle btn" aria-label = "Show secondary navigation" >
< i class = "bi bi-chevron-right" > < / i >
< / button >
< / div >
< / nav >
< / header >
<!-- content -->
< div id = "quarto-content" class = "quarto-container page-columns page-rows-contents page-layout-article" >
<!-- sidebar -->
< nav id = "quarto-sidebar" class = "sidebar collapse sidebar-navigation floating overflow-auto" >
< div class = "pt-lg-2 mt-2 text-left sidebar-header" >
< div class = "sidebar-title mb-0 py-0" >
< a href = "./" > OBITools V4< / a >
< / div >
< / div >
< div class = "mt-2 flex-shrink-0 align-items-center" >
< div class = "sidebar-search" >
< div id = "quarto-search" class = "" title = "Search" > < / div >
< / div >
< / div >
< div class = "sidebar-menu-container" >
< ul class = "list-unstyled mt-1" >
< li class = "sidebar-item" >
< div class = "sidebar-item-container" >
< a href = "./index.html" class = "sidebar-item-text sidebar-link" > Preface< / a >
< / div >
< / li >
< li class = "sidebar-item" >
< div class = "sidebar-item-container" >
< a href = "./intro.html" class = "sidebar-item-text sidebar-link" > < span class = "chapter-number" > 1< / span > < span class = "chapter-title" > The OBITools< / span > < / a >
< / div >
< / li >
< li class = "sidebar-item" >
< div class = "sidebar-item-container" >
2023-01-31 23:04:28 +01:00
< a href = "./tutorial.html" class = "sidebar-item-text sidebar-link" > < span class = "chapter-number" > 2< / span > < span class = "chapter-title" > OBITools V4 Tutorial< / span > < / a >
2023-01-17 19:06:14 +01:00
< / div >
< / li >
< li class = "sidebar-item" >
< div class = "sidebar-item-container" >
2023-01-31 23:04:28 +01:00
< a href = "./commands.html" class = "sidebar-item-text sidebar-link" > < span class = "chapter-number" > 3< / span > < span class = "chapter-title" > The < em > OBITools V4< / em > commands< / span > < / a >
2023-01-17 19:06:14 +01:00
< / div >
< / li >
< li class = "sidebar-item" >
< div class = "sidebar-item-container" >
2023-01-31 23:04:28 +01:00
< a href = "./library.html" class = "sidebar-item-text sidebar-link" > < span class = "chapter-number" > 4< / span > < span class = "chapter-title" > The GO < em > OBITools< / em > library< / span > < / a >
< / div >
< / li >
< li class = "sidebar-item" >
< div class = "sidebar-item-container" >
< a href = "./annexes.html" class = "sidebar-item-text sidebar-link" > < span class = "chapter-number" > 5< / span > < span class = "chapter-title" > Annexes< / span > < / a >
2023-01-17 19:06:14 +01:00
< / div >
< / li >
< li class = "sidebar-item" >
< div class = "sidebar-item-container" >
< a href = "./references.html" class = "sidebar-item-text sidebar-link active" > References< / a >
< / div >
< / li >
< / ul >
< / div >
< / nav >
<!-- margin - sidebar -->
< div id = "quarto-margin-sidebar" class = "sidebar margin-sidebar" >
< / div >
<!-- main -->
< main class = "content" id = "quarto-document-content" >
< header id = "title-block-header" class = "quarto-title-block default" >
< div class = "quarto-title" >
< h1 class = "title d-none d-lg-block" > References< / h1 >
< / div >
< div class = "quarto-title-meta" >
< / div >
< / header >
< div id = "refs" class = "references csl-bib-body hanging-indent" role = "doc-bibliography" >
2023-01-27 10:49:28 +01:00
< div id = "ref-Boyer2016-gq" class = "csl-entry" role = "doc-biblioentry" >
Boyer, Frédéric, Céline Mercier, Aurélie Bonin, Yvan Le Bras, Pierre
Taberlet, and Eric Coissac. 2016. < span > “< span class = "nocase" > obitools:
a unix-inspired software package for DNA metabarcoding< / span > .”< / span >
< em > Molecular Ecology Resources< / em > 16 (1): 176– 82. < a href = "https://doi.org/10.1111/1755-0998.12428" > https://doi.org/10.1111/1755-0998.12428< / a > .
< / div >
2023-01-17 19:06:14 +01:00
< div id = "ref-cock2010sanger" class = "csl-entry" role = "doc-biblioentry" >
Cock, Peter JA, Christopher J Fields, Naohisa Goto, Michael L Heuer, and
Peter M Rice. 2010. < span > “The Sanger FASTQ File Format for Sequences
with Quality Scores, and the Solexa/Illumina FASTQ Variants.”< / span >
< em > Nucleic Acids Research< / em > 38 (6): 1767– 71.
< / div >
2023-01-27 10:49:28 +01:00
< div id = "ref-Lipman1985-hw" class = "csl-entry" role = "doc-biblioentry" >
Lipman, D J, and W R Pearson. 1985. < span > “< span class = "nocase" > Rapid
and sensitive protein similarity searches< / span > .”< / span >
< em > Science< / em > 227 (4693): 1435– 41. < a href = "http://www.ncbi.nlm.nih.gov/pubmed/2983426" > http://www.ncbi.nlm.nih.gov/pubmed/2983426< / a > .
< / div >
2023-01-31 23:04:28 +01:00
< div id = "ref-Riaz2011-gn" class = "csl-entry" role = "doc-biblioentry" >
Riaz, Tiayyba, Wasim Shehzad, Alain Viari, François Pompanon, Pierre
Taberlet, and Eric Coissac. 2011. < span > “< span class = "nocase" > ecoPrimers: inference of new DNA barcode markers from
whole genome sequence analysis< / span > .”< / span > < em > Nucleic Acids
Research< / em > 39 (21): e145. < a href = "https://doi.org/10.1093/nar/gkr732" > https://doi.org/10.1093/nar/gkr732< / a > .
< / div >
< div id = "ref-Seguritan2001-tg" class = "csl-entry" role = "doc-biblioentry" >
Seguritan, V, and F Rohwer. 2001. < span > “< span class = "nocase" > FastGroup:
a program to dereplicate libraries of 16S rDNA sequences< / span > .”< / span >
< em > BMC Bioinformatics< / em > 2 (October): 9. < a href = "https://doi.org/10.1186/1471-2105-2-9" > https://doi.org/10.1186/1471-2105-2-9< / a > .
< / div >
< div id = "ref-Shehzad2012-pn" class = "csl-entry" role = "doc-biblioentry" >
Shehzad, Wasim, Tiayyba Riaz, Muhammad A Nawaz, Christian Miquel, Carole
Poillot, Safdar A Shah, Francois Pompanon, Eric Coissac, and Pierre
Taberlet. 2012. < span > “< span class = "nocase" > Carnivore diet analysis
based on next-generation sequencing: Application to the leopard cat
(Prionailurus bengalensis) in Pakistan< / span > .”< / span > < em > Molecular
Ecology< / em > 21 (8): 1951– 65. < a href = "https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2011.05424.x" > https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2011.05424.x< / a > .
< / div >
2023-01-17 19:06:14 +01:00
< / div >
< / main > <!-- /main -->
< script id = "quarto-html-after-body" type = "application/javascript" >
window.document.addEventListener("DOMContentLoaded", function (event) {
const toggleBodyColorMode = (bsSheetEl) => {
const mode = bsSheetEl.getAttribute("data-mode");
const bodyEl = window.document.querySelector("body");
if (mode === "dark") {
bodyEl.classList.add("quarto-dark");
bodyEl.classList.remove("quarto-light");
} else {
bodyEl.classList.add("quarto-light");
bodyEl.classList.remove("quarto-dark");
}
}
const toggleBodyColorPrimary = () => {
const bsSheetEl = window.document.querySelector("link#quarto-bootstrap");
if (bsSheetEl) {
toggleBodyColorMode(bsSheetEl);
}
}
toggleBodyColorPrimary();
const icon = "";
const anchorJS = new window.AnchorJS();
anchorJS.options = {
placement: 'right',
icon: icon
};
anchorJS.add('.anchored');
const clipboard = new window.ClipboardJS('.code-copy-button', {
target: function(trigger) {
return trigger.previousElementSibling;
}
});
clipboard.on('success', function(e) {
// button target
const button = e.trigger;
// don't keep focus
button.blur();
// flash "checked"
button.classList.add('code-copy-button-checked');
var currentTitle = button.getAttribute("title");
button.setAttribute("title", "Copied!");
let tooltip;
if (window.bootstrap) {
button.setAttribute("data-bs-toggle", "tooltip");
button.setAttribute("data-bs-placement", "left");
button.setAttribute("data-bs-title", "Copied!");
tooltip = new bootstrap.Tooltip(button,
{ trigger: "manual",
customClass: "code-copy-button-tooltip",
offset: [0, -8]});
tooltip.show();
}
setTimeout(function() {
if (tooltip) {
tooltip.hide();
button.removeAttribute("data-bs-title");
button.removeAttribute("data-bs-toggle");
button.removeAttribute("data-bs-placement");
}
button.setAttribute("title", currentTitle);
button.classList.remove('code-copy-button-checked');
}, 1000);
// clear code selection
e.clearSelection();
});
function tippyHover(el, contentFn) {
const config = {
allowHTML: true,
content: contentFn,
maxWidth: 500,
delay: 100,
arrow: false,
appendTo: function(el) {
return el.parentElement;
},
interactive: true,
interactiveBorder: 10,
theme: 'quarto',
placement: 'bottom-start'
};
window.tippy(el, config);
}
const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
for (var i=0; i< noterefs.length ; i + + ) {
const ref = noterefs[i];
tippyHover(ref, function() {
// use id or data attribute instead here
let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href');
try { href = new URL(href).hash; } catch {}
const id = href.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
return note.innerHTML;
});
}
const findCites = (el) => {
const parentEl = el.parentElement;
if (parentEl) {
const cites = parentEl.dataset.cites;
if (cites) {
return {
el,
cites: cites.split(' ')
};
} else {
return findCites(el.parentElement)
}
} else {
return undefined;
}
};
var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
for (var i=0; i< bibliorefs.length ; i + + ) {
const ref = bibliorefs[i];
const citeInfo = findCites(ref);
if (citeInfo) {
tippyHover(citeInfo.el, function() {
var popup = window.document.createElement('div');
citeInfo.cites.forEach(function(cite) {
var citeDiv = window.document.createElement('div');
citeDiv.classList.add('hanging-indent');
citeDiv.classList.add('csl-entry');
var biblioDiv = window.document.getElementById('ref-' + cite);
if (biblioDiv) {
citeDiv.innerHTML = biblioDiv.innerHTML;
}
popup.appendChild(citeDiv);
});
return popup.innerHTML;
});
}
}
});
< / script >
< nav class = "page-navigation" >
< div class = "nav-page nav-page-previous" >
< a href = "./annexes.html" class = "pagination-link" >
2023-01-31 23:04:28 +01:00
< i class = "bi bi-arrow-left-short" > < / i > < span class = "nav-page-text" > < span class = "chapter-number" > 5< / span > < span class = "chapter-title" > Annexes< / span > < / span >
2023-01-17 19:06:14 +01:00
< / a >
< / div >
< div class = "nav-page nav-page-next" >
< / div >
< / nav >
< / div > <!-- /content -->
< / body > < / html >