http://stab.st-andrews.ac.uk/wiki/index.php?title=Synthetic_Long_reads&feed=atom&action=historySynthetic Long reads - Revision history2024-03-28T16:55:33ZRevision history for this page on the wikiMediaWiki 1.30.0http://stab.st-andrews.ac.uk/wiki/index.php?title=Synthetic_Long_reads&diff=128&oldid=prevRf at 16:02, 8 April 20162016-04-08T16:02:19Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>It is already installed on the Bioinformatics cluster to ensure fast processing. The pipeline starts by synthesising long reads by mapping the short read to the barcoded pools. Next, a de Bruijn graph - a compact representation of the long reads in their order of sequence - is iteratively refined into scaffolds through a series of error-correction and coverage gap-filling stages. The resulting de-novo assembly is of higher resolution than can be achieved with a higher percentage of spanned gaps and errors corrected.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>It is already installed on the Bioinformatics cluster to ensure fast processing. The pipeline starts by synthesising long reads by mapping the short read to the barcoded pools. Next, a de Bruijn graph - a compact representation of the long reads in their order of sequence - is iteratively refined into scaffolds through a series of error-correction and coverage gap-filling stages. The resulting de-novo assembly is of higher resolution than can be achieved with a higher percentage of spanned gaps and errors corrected.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">The general procedure for synthetic long reads is as follows:</ins></div></td></tr>
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</table>Rfhttp://stab.st-andrews.ac.uk/wiki/index.php?title=Synthetic_Long_reads&diff=126&oldid=prevRf at 15:34, 8 April 20162016-04-08T15:34:02Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>It is already installed on the Bioinformatics cluster to ensure fast processing. The pipeline starts by synthesising long reads by mapping the short read to the barcoded pools. Next, a de Bruijn graph - a compact representation of the long reads in their order of sequence - is iteratively refined into scaffolds through a series of error-correction and coverage gap-filling stages. The resulting de-novo assembly is of higher resolution than can be achieved with a higher percentage of spanned gaps and errors corrected.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>It is already installed on the Bioinformatics cluster to ensure fast processing. The pipeline starts by synthesising long reads by mapping the short read to the barcoded pools. Next, a de Bruijn graph - a compact representation of the long reads in their order of sequence - is iteratively refined into scaffolds through a series of error-correction and coverage gap-filling stages. The resulting de-novo assembly is of higher resolution than can be achieved with a higher percentage of spanned gaps and errors corrected.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Ref</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Bankevich, A.  and Pevzner, P. A. (2016) TruSPAdes: barcode assembly of TruSeq synthetic long reads, Nature Methods 3: 248-250.</del></div></td><td colspan="2"> </td></tr>
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</table>Rfhttp://stab.st-andrews.ac.uk/wiki/index.php?title=Synthetic_Long_reads&diff=125&oldid=prevRf at 15:33, 8 April 20162016-04-08T15:33:37Z<p></p>
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<td colspan="2" style="background-color: white; color:black; text-align: center;">Revision as of 15:33, 8 April 2016</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l3" >Line 3:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>A recent development, synthetic long reads have already been used successfully in projects for complex transposon resolution, recovery of missing sequences, metagenomics and exome enrichment.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>A recent development, synthetic long reads have already been used successfully in projects for complex transposon resolution, recovery of missing sequences, metagenomics and exome enrichment.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The goal of the bioinformatics pipeline is to produce a de-novo assembly of higher resolution where sequencing gaps can be correctly bridged by virtue of the increase read length. One software that can be used is the enhancement of the widely used '''SPAdes''' program called '''TruSPAdes''' which is focused on handling the particular challenge of assembling synthetic long reads, such as handling and correcting chimeric reads</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The goal of the bioinformatics pipeline is to produce a de-novo assembly of higher resolution where sequencing gaps can be correctly bridged by virtue of the increase read length. One software that can be used is the enhancement of the widely used '''SPAdes''' program called '''TruSPAdes'''<ins class="diffchange diffchange-inline"><ref>Bankevich, A.  and Pevzner, P. A. (2016) TruSPAdes: barcode assembly of TruSeq synthetic long reads, Nature Methods 3: 248-250</ref> </ins>which is focused on handling the particular challenge of assembling synthetic long reads, such as handling and correcting chimeric reads</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>It is already installed on the Bioinformatics cluster to ensure fast processing. The pipeline starts by synthesising long reads by mapping the short read to the barcoded pools. Next, a de Bruijn graph - a compact representation of the long reads in their order of sequence - is iteratively refined into scaffolds through a series of error-correction and coverage gap-filling stages. The resulting de-novo assembly is of higher resolution than can be achieved with a higher percentage of spanned gaps and errors corrected.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>It is already installed on the Bioinformatics cluster to ensure fast processing. The pipeline starts by synthesising long reads by mapping the short read to the barcoded pools. Next, a de Bruijn graph - a compact representation of the long reads in their order of sequence - is iteratively refined into scaffolds through a series of error-correction and coverage gap-filling stages. The resulting de-novo assembly is of higher resolution than can be achieved with a higher percentage of spanned gaps and errors corrected.</div></td></tr>
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</table>Rfhttp://stab.st-andrews.ac.uk/wiki/index.php?title=Synthetic_Long_reads&diff=123&oldid=prevRf at 15:12, 8 April 20162016-04-08T15:12:16Z<p></p>
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<td colspan="2" style="background-color: white; color:black; text-align: center;">Revision as of 15:12, 8 April 2016</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td>
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<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>NGS reads are short in that they found in the 50-200 base-pair length scale. Longer reads are seen as more powerful, so there is a general tendency towards longer reads which is reflected in prices. Illumina generally have focussed on shorter reads, but in an effort to follow trends, they have the developed the ''synthetic'' long read.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>NGS reads are <ins class="diffchange diffchange-inline">typically </ins>short in that they found in the 50-200 base-pair length scale. Longer reads are seen as more powerful, so there is a general tendency towards longer reads which is reflected in prices. Illumina generally have focussed on shorter reads, but in an effort to follow trends, they have the developed the ''synthetic'' long read.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>A recent development, synthetic long reads have already been used successfully in projects for complex transposon resolution, recovery of missing sequences, metagenomics and exome enrichment.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>A recent development, synthetic long reads have already been used successfully in projects for complex transposon resolution, recovery of missing sequences, metagenomics and exome enrichment.</div></td></tr>
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</table>Rfhttp://stab.st-andrews.ac.uk/wiki/index.php?title=Synthetic_Long_reads&diff=122&oldid=prevRf: Created page with "NGS reads are short in that they found in the 50-200 base-pair length scale. Longer reads are seen as more powerful, so there is a general tendency towards longer reads which..."2016-04-08T15:01:47Z<p>Created page with "NGS reads are short in that they found in the 50-200 base-pair length scale. Longer reads are seen as more powerful, so there is a general tendency towards longer reads which..."</p>
<p><b>New page</b></p><div>NGS reads are short in that they found in the 50-200 base-pair length scale. Longer reads are seen as more powerful, so there is a general tendency towards longer reads which is reflected in prices. Illumina generally have focussed on shorter reads, but in an effort to follow trends, they have the developed the ''synthetic'' long read.<br />
<br />
A recent development, synthetic long reads have already been used successfully in projects for complex transposon resolution, recovery of missing sequences, metagenomics and exome enrichment.<br />
<br />
The goal of the bioinformatics pipeline is to produce a de-novo assembly of higher resolution where sequencing gaps can be correctly bridged by virtue of the increase read length. One software that can be used is the enhancement of the widely used '''SPAdes''' program called '''TruSPAdes''' which is focused on handling the particular challenge of assembling synthetic long reads, such as handling and correcting chimeric reads<br />
<br />
It is already installed on the Bioinformatics cluster to ensure fast processing. The pipeline starts by synthesising long reads by mapping the short read to the barcoded pools. Next, a de Bruijn graph - a compact representation of the long reads in their order of sequence - is iteratively refined into scaffolds through a series of error-correction and coverage gap-filling stages. The resulting de-novo assembly is of higher resolution than can be achieved with a higher percentage of spanned gaps and errors corrected.<br />
<br />
Ref<br />
<br />
Bankevich, A. and Pevzner, P. A. (2016) TruSPAdes: barcode assembly of TruSeq synthetic long reads, Nature Methods 3: 248-250.</div>Rf