Table 1.
Draft and multiplatform assemblies generated for the paradise crow; for each assembly the sequencing technology and software used to produce them are shown together with contig N50, scaffold N50 and the number of gaps
| Assembly | Technology | Software | Contig N50 (bp) | No. of contigs | Scaffold N50 (bp) | No. of scaffolds | No. of gaps a | Missing assembly b (%) |
|---|---|---|---|---|---|---|---|---|
| lycPyrIL | Illumina HiSeq2500 (PE + MP) | allpaths‐lg | 620,719 | 10,766 | 4,227,710 | 3,216 | 14,573 | 3.82 |
| lycPyrPB | PacBio RSII C6‐P4 | falcon | 6,644,420 | 3,422 | — | — | — | 0.45 |
| lycPyrSN1 | 10X Genomics Chromium HiSeqX | supernova2 | 144,856 | 29,791 | 4,360,585 | 13,934 | 21,550 | 4.53 |
| lycPyrSN2 | 10X Genomics Chromium HiSeqX | supernova2 | 149,640 | 27,366 | 4,748,626 | 14,217 | 20,131 | 2.62 |
| lycPyrHiC | PacBio + Phase Genomics Hi‐C | proximo | 6,644,420 | 3,422 | 70,588,898 | 2,927 | 533 | 0.45 |
| lycPyrILPB | lycPyrIL + gap‐filling with PacBio | pbjelly | 1,982,606 | 6,895 | 4,229,628 | 3,216 | 10,422 | 3.03 |
| lycPyr2 | PacBio + Dovetail CHiCAGO | hirise | 6,294,665 | 3,463 | 6,644,037 | 3,227 | 282 | 0.45 |
| lycPyr3 | lycPyr2 + 10X Genomics | arcs + links | 6,294,665 | 3,463 | 8,009,555 | 3,121 | 345 | 0.27 |
| lycPyr4 | lycPyr3 + Phase Genomics Hi‐C | proximo | 6,294,665 | 3,463 | 69,071,023 | 1,713 | 1,791 | 0.27 |
| lycPyr5 | lycPyr4 + manual curation with alignments + gap filling | pbjelly | 7,540,011 | 3,269 | 74,173,823 | 1,700 | 1,631 | 0.001 |
| lycPyr6 | lycPyr5 + manual curation with Hi‐C | juicer | 7,540,011 | 3,271 | 74,173,823 | 1,700 | 1,635 | — |
Abbreviations: MP, mate pair reads; PE, paired end reads.
a
The number of gaps is estimated as the count of stretches of N nucleotides within a scaffold.
b
The percentage of incompleteness is relative to the final version of the multiplatform assembly: (1 − (assembly size/final assembly size)) × 100. The N nucleotides are excluded from the calculation.