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#About ItrAs

This is a software tool relying on GATB-CORE library. It essentially copies the theory behind IDBA-UD

It uses the backbone of Minia though to do iterative kmer assemly. You specify and minimum k, a maximum k, and a step size. The assembler will then build a graph for the mink size and produce contigs. The contigs and the read file are then used to build the next graph where new contigs are produced. These contigs along with reads are used to build the next graph... and so on. The final contigs are in the file 'contig.fa' in the output folder.

It has Karect Read Error correction integrated (enabled with -pre_correct 1). Karect is limited to the free amount of RAM on the machine you run on.

To build, just type 'make'

To Test, type 'make test' - This will run the program on the GAGE Staphylococcus aureus AllPaths corrected dataset. (located in tests folder)

To run, specify the minimum k, maximum k, step size, input file and output directory. ./build/tools/ItrAs --help (to show all options)

Example: ./build/tools/ItrAs -in inputfile.fa -mink 35 -step 10 -maxk 95 -out OutputDir

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Iterative Genome Assembly using GATB library

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assemblygatbgenomeiterative

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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#About ItrAs
This is a software tool relying on GATB-CORE library. It essentially copies the theory behind IDBA-UD
It uses the backbone of Minia though to do iterative kmer assemly. You specify and minimum k, a maximum k, and a step size. The assembler will then build a graph for the mink size and produce contigs. The contigs and the read file are then used to build the next graph where new contigs are produced. These contigs along with reads are used to build the next graph... and so on. The final contigs are in the file 'contig.fa' in the output folder.
It has Karect Read Error correction integrated (enabled with -pre_correct 1). Karect is limited to the free amount of RAM on the machine you run on.
To build, just type 'make'
To Test, type 'make test' - This will run the program on the GAGE Staphylococcus aureus AllPaths corrected dataset. (located in tests folder)
To run, specify the minimum k, maximum k, step size, input file and output directory.
./build/tools/ItrAs --help (to show all options)
Example:
./build/tools/ItrAs -in inputfile.fa -mink 35 -step 10 -maxk 95 -out OutputDir
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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#About ItrAs
This is a software tool relying on GATB-CORE library. It essentially copies the theory behind IDBA-UD
It uses the backbone of Minia though to do iterative kmer assemly. You specify and minimum k, a maximum k, and a step size. The assembler will then build a graph for the mink size and produce contigs. The contigs and the read file are then used to build the next graph where new contigs are produced. These contigs along with reads are used to build the next graph... and so on. The final contigs are in the file 'contig.fa' in the output folder.
It has Karect Read Error correction integrated (enabled with -pre_correct 1). Karect is limited to the free amount of RAM on the machine you run on.
To build, just type 'make'
To Test, type 'make test' - This will run the program on the GAGE Staphylococcus aureus AllPaths corrected dataset. (located in tests folder)
To run, specify the minimum k, maximum k, step size, input file and output directory.
./build/tools/ItrAs --help (to show all options)
Example:
./build/tools/ItrAs -in inputfile.fa -mink 35 -step 10 -maxk 95 -out OutputDir
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Iterative Genome Assembly using GATB library
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assemblygatbgenomeiterative
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Readme
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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#About ItrAs
This is a software tool relying on GATB-CORE library. It essentially copies the theory behind IDBA-UD
It uses the backbone of Minia though to do iterative kmer assemly. You specify and minimum k, a maximum k, and a step size. The assembler will then build a graph for the mink size and produce contigs. The contigs and the read file are then used to build the next graph where new contigs are produced. These contigs along with reads are used to build the next graph... and so on. The final contigs are in the file 'contig.fa' in the output folder.
It has Karect Read Error correction integrated (enabled with -pre_correct 1). Karect is limited to the free amount of RAM on the machine you run on.
To build, just type 'make'
To Test, type 'make test' - This will run the program on the GAGE Staphylococcus aureus AllPaths corrected dataset. (located in tests folder)
To run, specify the minimum k, maximum k, step size, input file and output directory.
./build/tools/ItrAs --help (to show all options)
Example:
./build/tools/ItrAs -in inputfile.fa -mink 35 -step 10 -maxk 95 -out OutputDir
About
Iterative Genome Assembly using GATB library
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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Repository files navigation
#About ItrAs
This is a software tool relying on GATB-CORE library. It essentially copies the theory behind IDBA-UD
It uses the backbone of Minia though to do iterative kmer assemly. You specify and minimum k, a maximum k, and a step size. The assembler will then build a graph for the mink size and produce contigs. The contigs and the read file are then used to build the next graph where new contigs are produced. These contigs along with reads are used to build the next graph... and so on. The final contigs are in the file 'contig.fa' in the output folder.
It has Karect Read Error correction integrated (enabled with -pre_correct 1). Karect is limited to the free amount of RAM on the machine you run on.
To build, just type 'make'
To Test, type 'make test' - This will run the program on the GAGE Staphylococcus aureus AllPaths corrected dataset. (located in tests folder)
To run, specify the minimum k, maximum k, step size, input file and output directory.
./build/tools/ItrAs --help (to show all options)
Example:
./build/tools/ItrAs -in inputfile.fa -mink 35 -step 10 -maxk 95 -out OutputDir
About
Iterative Genome Assembly using GATB library
Topics
assemblygatbgenomeiterative
Resources
Readme
AGPL-3.0 license
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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#About ItrAs
This is a software tool relying on GATB-CORE library. It essentially copies the theory behind IDBA-UD
It uses the backbone of Minia though to do iterative kmer assemly. You specify and minimum k, a maximum k, and a step size. The assembler will then build a graph for the mink size and produce contigs. The contigs and the read file are then used to build the next graph where new contigs are produced. These contigs along with reads are used to build the next graph... and so on. The final contigs are in the file 'contig.fa' in the output folder.
It has Karect Read Error correction integrated (enabled with -pre_correct 1). Karect is limited to the free amount of RAM on the machine you run on.
To build, just type 'make'
To Test, type 'make test' - This will run the program on the GAGE Staphylococcus aureus AllPaths corrected dataset. (located in tests folder)
To run, specify the minimum k, maximum k, step size, input file and output directory.
./build/tools/ItrAs --help (to show all options)
Example:
./build/tools/ItrAs -in inputfile.fa -mink 35 -step 10 -maxk 95 -out OutputDir
About
Iterative Genome Assembly using GATB library
Topics
assemblygatbgenomeiterative
Resources
Readme
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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#About ItrAs
This is a software tool relying on GATB-CORE library. It essentially copies the theory behind IDBA-UD
It uses the backbone of Minia though to do iterative kmer assemly. You specify and minimum k, a maximum k, and a step size. The assembler will then build a graph for the mink size and produce contigs. The contigs and the read file are then used to build the next graph where new contigs are produced. These contigs along with reads are used to build the next graph... and so on. The final contigs are in the file 'contig.fa' in the output folder.
It has Karect Read Error correction integrated (enabled with -pre_correct 1). Karect is limited to the free amount of RAM on the machine you run on.
To build, just type 'make'
To Test, type 'make test' - This will run the program on the GAGE Staphylococcus aureus AllPaths corrected dataset. (located in tests folder)
To run, specify the minimum k, maximum k, step size, input file and output directory.
./build/tools/ItrAs --help (to show all options)
Example:
./build/tools/ItrAs -in inputfile.fa -mink 35 -step 10 -maxk 95 -out OutputDir
About
Iterative Genome Assembly using GATB library
Topics
assemblygatbgenomeiterative
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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#About ItrAs
This is a software tool relying on GATB-CORE library. It essentially copies the theory behind IDBA-UD
It uses the backbone of Minia though to do iterative kmer assemly. You specify and minimum k, a maximum k, and a step size. The assembler will then build a graph for the mink size and produce contigs. The contigs and the read file are then used to build the next graph where new contigs are produced. These contigs along with reads are used to build the next graph... and so on. The final contigs are in the file 'contig.fa' in the output folder.
It has Karect Read Error correction integrated (enabled with -pre_correct 1). Karect is limited to the free amount of RAM on the machine you run on.
To build, just type 'make'
To Test, type 'make test' - This will run the program on the GAGE Staphylococcus aureus AllPaths corrected dataset. (located in tests folder)
To run, specify the minimum k, maximum k, step size, input file and output directory.
./build/tools/ItrAs --help (to show all options)
Example:
./build/tools/ItrAs -in inputfile.fa -mink 35 -step 10 -maxk 95 -out OutputDir
About
Iterative Genome Assembly using GATB library
Topics
assemblygatbgenomeiterative
Resources
Readme
AGPL-3.0 license
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