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This repository contains software for evaluation of spliced aligners, written to assess RNA-seq mappers as part of the RGASP project.

Some of the scripts are tailored to particular data sets analyzed in RGASP or to the computational environment at the European Bioinformatics Institute, where the RGASP evaluation was carried out.

The evaluation considered alignments of both real and simulated RNA-seq data. The simulated data was generated using the BEERS simulator, and evaluated using the scripts in this repository. Some of the scripts herein specifically deal with alignments of simulated data, extracting accuracy metrics by comparison with the true alignments and/or simulated transcript models. Other scripts extract more general alignment statistics, and can be applied both to alignments of real and simulated data. Most scripts that process alignments expect input in SAM or BAM format.

A subset of the software written for the RGASP spliced aligner evaluation are in a separate repository: https://github.com/RGASP-consortium/coverage. These scripts extract metrics relating to the coverage of genomic features by alignments, and produce plots of those metrics.

Dependencies:

  • Genoman - perl library required by some of the perl scripts
  • SAMTools - for BAM file I/O
  • R packages: gplots, plotrix, RColorBrewer

Please see further documentation under the doc directory.

If using this software, please cite:
Engström et al. (2013) Systematic evaluation of spliced alignment programs for RNA-seq data. Nat Methods, in press.

If you have questions about this software, please write to par.engstrom@scilifelab.se.

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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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This repository contains software for evaluation of spliced aligners,
written to assess RNA-seq mappers as part of the RGASP project.
Some of the scripts are tailored to particular data sets analyzed in
RGASP or to the computational environment at the European
Bioinformatics Institute, where the RGASP evaluation was carried out.
The evaluation considered alignments of both real and simulated
RNA-seq data. The simulated data was generated using the BEERS
simulator, and evaluated using the scripts in this repository. Some of
the scripts herein specifically deal with alignments of simulated
data, extracting accuracy metrics by comparison with the true
alignments and/or simulated transcript models. Other scripts extract
more general alignment statistics, and can be applied both to
alignments of real and simulated data. Most scripts that process
alignments expect input in SAM or BAM format.
A subset of the software written for the RGASP spliced aligner
evaluation are in a separate repository:
https://github.com/RGASP-consortium/coverage.
These scripts extract metrics relating to the coverage of genomic
features by alignments, and produce plots of those metrics.
Dependencies:
  • Genoman - perl library required by some of the perl scripts
  • SAMTools - for BAM file I/O
  • R packages: gplots, plotrix, RColorBrewer
Please see further documentation under the doc directory.
If using this software, please cite:

Engström et al. (2013) Systematic evaluation of spliced alignment
programs for RNA-seq data. Nat Methods, in press.
If you have questions about this software, please write to
par.engstrom@scilifelab.se.
About
Spliced alignment evaluation software
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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); }
})();
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var __m = "*";
var __re = new RegExp('^' + ".*" + '

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This repository contains software for evaluation of spliced aligners,
written to assess RNA-seq mappers as part of the RGASP project.
Some of the scripts are tailored to particular data sets analyzed in
RGASP or to the computational environment at the European
Bioinformatics Institute, where the RGASP evaluation was carried out.
The evaluation considered alignments of both real and simulated
RNA-seq data. The simulated data was generated using the BEERS
simulator, and evaluated using the scripts in this repository. Some of
the scripts herein specifically deal with alignments of simulated
data, extracting accuracy metrics by comparison with the true
alignments and/or simulated transcript models. Other scripts extract
more general alignment statistics, and can be applied both to
alignments of real and simulated data. Most scripts that process
alignments expect input in SAM or BAM format.
A subset of the software written for the RGASP spliced aligner
evaluation are in a separate repository:
https://github.com/RGASP-consortium/coverage.
These scripts extract metrics relating to the coverage of genomic
features by alignments, and produce plots of those metrics.
Dependencies:
  • Genoman - perl library required by some of the perl scripts
  • SAMTools - for BAM file I/O
  • R packages: gplots, plotrix, RColorBrewer
Please see further documentation under the doc directory.
If using this software, please cite:

Engström et al. (2013) Systematic evaluation of spliced alignment
programs for RNA-seq data. Nat Methods, in press.
If you have questions about this software, please write to
par.engstrom@scilifelab.se.
About
Spliced alignment evaluation software
Resources
Readme
Activity
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1 watching
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3 forks
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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); }
})();
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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This repository contains software for evaluation of spliced aligners,
written to assess RNA-seq mappers as part of the RGASP project.
Some of the scripts are tailored to particular data sets analyzed in
RGASP or to the computational environment at the European
Bioinformatics Institute, where the RGASP evaluation was carried out.
The evaluation considered alignments of both real and simulated
RNA-seq data. The simulated data was generated using the BEERS
simulator, and evaluated using the scripts in this repository. Some of
the scripts herein specifically deal with alignments of simulated
data, extracting accuracy metrics by comparison with the true
alignments and/or simulated transcript models. Other scripts extract
more general alignment statistics, and can be applied both to
alignments of real and simulated data. Most scripts that process
alignments expect input in SAM or BAM format.
A subset of the software written for the RGASP spliced aligner
evaluation are in a separate repository:
https://github.com/RGASP-consortium/coverage.
These scripts extract metrics relating to the coverage of genomic
features by alignments, and produce plots of those metrics.
Dependencies:
  • Genoman - perl library required by some of the perl scripts
  • SAMTools - for BAM file I/O
  • R packages: gplots, plotrix, RColorBrewer
Please see further documentation under the doc directory.
If using this software, please cite:

Engström et al. (2013) Systematic evaluation of spliced alignment
programs for RNA-seq data. Nat Methods, in press.
If you have questions about this software, please write to
par.engstrom@scilifelab.se.
About
Spliced alignment evaluation software
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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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This repository contains software for evaluation of spliced aligners,
written to assess RNA-seq mappers as part of the RGASP project.
Some of the scripts are tailored to particular data sets analyzed in
RGASP or to the computational environment at the European
Bioinformatics Institute, where the RGASP evaluation was carried out.
The evaluation considered alignments of both real and simulated
RNA-seq data. The simulated data was generated using the BEERS
simulator, and evaluated using the scripts in this repository. Some of
the scripts herein specifically deal with alignments of simulated
data, extracting accuracy metrics by comparison with the true
alignments and/or simulated transcript models. Other scripts extract
more general alignment statistics, and can be applied both to
alignments of real and simulated data. Most scripts that process
alignments expect input in SAM or BAM format.
A subset of the software written for the RGASP spliced aligner
evaluation are in a separate repository:
https://github.com/RGASP-consortium/coverage.
These scripts extract metrics relating to the coverage of genomic
features by alignments, and produce plots of those metrics.
Dependencies:
  • Genoman - perl library required by some of the perl scripts
  • SAMTools - for BAM file I/O
  • R packages: gplots, plotrix, RColorBrewer
Please see further documentation under the doc directory.
If using this software, please cite:

Engström et al. (2013) Systematic evaluation of spliced alignment
programs for RNA-seq data. Nat Methods, in press.
If you have questions about this software, please write to
par.engstrom@scilifelab.se.
About
Spliced alignment evaluation software
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Readme
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3 forks
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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); }
})();
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var __m = "*";
var __re = new RegExp('^' + ".*" + '

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This repository contains software for evaluation of spliced aligners,
written to assess RNA-seq mappers as part of the RGASP project.
Some of the scripts are tailored to particular data sets analyzed in
RGASP or to the computational environment at the European
Bioinformatics Institute, where the RGASP evaluation was carried out.
The evaluation considered alignments of both real and simulated
RNA-seq data. The simulated data was generated using the BEERS
simulator, and evaluated using the scripts in this repository. Some of
the scripts herein specifically deal with alignments of simulated
data, extracting accuracy metrics by comparison with the true
alignments and/or simulated transcript models. Other scripts extract
more general alignment statistics, and can be applied both to
alignments of real and simulated data. Most scripts that process
alignments expect input in SAM or BAM format.
A subset of the software written for the RGASP spliced aligner
evaluation are in a separate repository:
https://github.com/RGASP-consortium/coverage.
These scripts extract metrics relating to the coverage of genomic
features by alignments, and produce plots of those metrics.
Dependencies:
  • Genoman - perl library required by some of the perl scripts
  • SAMTools - for BAM file I/O
  • R packages: gplots, plotrix, RColorBrewer
Please see further documentation under the doc directory.
If using this software, please cite:

Engström et al. (2013) Systematic evaluation of spliced alignment
programs for RNA-seq data. Nat Methods, in press.
If you have questions about this software, please write to
par.engstrom@scilifelab.se.
About
Spliced alignment evaluation software
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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");
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} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
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var __m = "*";
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This repository contains software for evaluation of spliced aligners,
written to assess RNA-seq mappers as part of the RGASP project.
Some of the scripts are tailored to particular data sets analyzed in
RGASP or to the computational environment at the European
Bioinformatics Institute, where the RGASP evaluation was carried out.
The evaluation considered alignments of both real and simulated
RNA-seq data. The simulated data was generated using the BEERS
simulator, and evaluated using the scripts in this repository. Some of
the scripts herein specifically deal with alignments of simulated
data, extracting accuracy metrics by comparison with the true
alignments and/or simulated transcript models. Other scripts extract
more general alignment statistics, and can be applied both to
alignments of real and simulated data. Most scripts that process
alignments expect input in SAM or BAM format.
A subset of the software written for the RGASP spliced aligner
evaluation are in a separate repository:
https://github.com/RGASP-consortium/coverage.
These scripts extract metrics relating to the coverage of genomic
features by alignments, and produce plots of those metrics.
Dependencies:
  • Genoman - perl library required by some of the perl scripts
  • SAMTools - for BAM file I/O
  • R packages: gplots, plotrix, RColorBrewer
Please see further documentation under the doc directory.
If using this software, please cite:

Engström et al. (2013) Systematic evaluation of spliced alignment
programs for RNA-seq data. Nat Methods, in press.
If you have questions about this software, please write to
par.engstrom@scilifelab.se.
About
Spliced alignment evaluation software
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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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This repository contains software for evaluation of spliced aligners,
written to assess RNA-seq mappers as part of the RGASP project.
Some of the scripts are tailored to particular data sets analyzed in
RGASP or to the computational environment at the European
Bioinformatics Institute, where the RGASP evaluation was carried out.
The evaluation considered alignments of both real and simulated
RNA-seq data. The simulated data was generated using the BEERS
simulator, and evaluated using the scripts in this repository. Some of
the scripts herein specifically deal with alignments of simulated
data, extracting accuracy metrics by comparison with the true
alignments and/or simulated transcript models. Other scripts extract
more general alignment statistics, and can be applied both to
alignments of real and simulated data. Most scripts that process
alignments expect input in SAM or BAM format.
A subset of the software written for the RGASP spliced aligner
evaluation are in a separate repository:
https://github.com/RGASP-consortium/coverage.
These scripts extract metrics relating to the coverage of genomic
features by alignments, and produce plots of those metrics.
Dependencies:
  • Genoman - perl library required by some of the perl scripts
  • SAMTools - for BAM file I/O
  • R packages: gplots, plotrix, RColorBrewer
Please see further documentation under the doc directory.
If using this software, please cite:

Engström et al. (2013) Systematic evaluation of spliced alignment
programs for RNA-seq data. Nat Methods, in press.
If you have questions about this software, please write to
par.engstrom@scilifelab.se.
About
Spliced alignment evaluation software
Resources
Readme
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3 forks
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