Genome Assemblies: Difference between revisions
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We sought to improve the Patiria miniata genome assembly with additional PacBio sequences. We generated a new PacBio read dataset at the Duke University Sequencing Center using our reference individual DNA. The read dataset contains 2 million reads and 15.8 billion bp. The read N50 is 10.4 Kb. We used PBJelly2 to combine the PacBio reads with the previously assembled contigs. The results were an improvement in contig size and number with only a small reduction in the number of scaffolds (Table). The P. miniata Gene v2.0 set was generated using MAKER2 pipeline from v2.0 genome assembly. | We sought to improve the Patiria miniata genome assembly with additional PacBio sequences. We generated a new PacBio read dataset at the Duke University Sequencing Center using our reference individual DNA. The read dataset contains 2 million reads and 15.8 billion bp. The read N50 is 10.4 Kb. We used PBJelly2 to combine the PacBio reads with the previously assembled contigs. The results were an improvement in contig size and number with only a small reduction in the number of scaffolds (Table). The P. miniata Gene v2.0 set was generated using MAKER2 pipeline from v2.0 genome assembly. | ||
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< | <table class="tg"> | ||
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<th class="tg-cly1"></th> | |||
< | <th class="tg-0lax">Pm v1.0</th> | ||
< | <th class="tg-0lax">Pm v2.0</th> | ||
</tr> | |||
< | |||
<tr> | <tr> | ||
< | <td class="tg-0lax">Scaffold number</td> | ||
< | <td class="tg-0lax">60,183</td> | ||
< | <td class="tg-0lax">57,698</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td> | <td class="tg-0lax">Scaffold N50</td> | ||
<td> | <td class="tg-0lax">52,6141</td> | ||
<td> | <td class="tg-0lax">76,341</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td> | <td class="tg-0lax">Contig number</td> | ||
<td> | <td class="tg-0lax">179,756</td> | ||
<td> | <td class="tg-0lax">131,779</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td> | <td class="tg-0lax">Contig N50</td> | ||
<td> | <td class="tg-0lax">9,466</td> | ||
<td> | <td class="tg-0lax">18,676</td> | ||
</tr> | </tr> | ||
</table> | </table> | ||
Revision as of 13:31, 4 December 2019
Echinoderm Genome Assemblies by Species
Strongylocentrotus purpuratus
Assembly_3.1 (Spur_3.1)
Assembly 2.6(Spur 2.6)
Assembly_2.5(Spur_2.5)
Assembly_2.1(Spur_2.1)
Assembly_0.5(Spur_0.5)
Patiria miniata
V2.0 Assembly
We sought to improve the Patiria miniata genome assembly with additional PacBio sequences. We generated a new PacBio read dataset at the Duke University Sequencing Center using our reference individual DNA. The read dataset contains 2 million reads and 15.8 billion bp. The read N50 is 10.4 Kb. We used PBJelly2 to combine the PacBio reads with the previously assembled contigs. The results were an improvement in contig size and number with only a small reduction in the number of scaffolds (Table). The P. miniata Gene v2.0 set was generated using MAKER2 pipeline from v2.0 genome assembly.
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.tg {border-collapse:collapse;border-spacing:0;}
.tg td{font-family:Arial, sans-serif;font-size:14px;padding:5px 20px;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;border-color:black;}
.tg th{font-family:Arial, sans-serif;font-size:14px;font-weight:normal;padding:5px 20px;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;border-color:black;}
.tg .tg-cly1{text-align:left;vertical-align:middle}
.tg .tg-0lax{text-align:left;vertical-align:top}
</style>
| Pm v1.0 | Pm v2.0 | |
|---|---|---|
| Scaffold number | 60,183 | 57,698 |
| Scaffold N50 | 52,6141 | 76,341 |
| Contig number | 179,756 | 131,779 |
| Contig N50 | 9,466 | 18,676 |