Modified data: v2#

Some input data for whom khloraascaf failed the scaffolding have been minimally modified.

Agathis_dammara#

  • \(1_{mult} \gets 3\)

Begonia_pulchrifolia#

  • The starter becomes contig \(4\)

    • Arbitrary, it could be all but contig \(0\)

  • \(1_{mult} = 2_{mult} = 3_{mult} = 4_{mult} = 5_{mult} = 1\) and \(0_{mult} = 2\)

    • According to the same calculus from coverage to multiplicity as the one for original input data

Carpodetus_serratus#

  • #TODO prefer transforming the links into contigs, and add new links between, change the sequences

  • remove just one link: \(10_r 11_f\)

Cucumix_hystrix#

Cannot change something to solve this issue

Jasminum_tortuosum#

  • Add link \((6_f, 4_f)\)

Lamprocapnos_spectabilis#

  • The starter becomes contig \(8\)

    • It cannot be contig \(5\) or contig \(7\) as contig \(0\) could be under-estimated: \(8_{cov} = 115 < 5_{cov} = 121 < 7_{cov} = 122\) and \(0_{cov} = 243\)

  • Multiplicities for contig \(2\), contig \(4\), contig \(6\), contig \(10\), contig \(11\) increase by \(1\)

  • Multiplicities for contig \(0\), contig \(1\), contig \(3\) increase by \(2\)

Lathyrus_pubescens#

  • \(12_{prob} \gets 0.01\)

    • The calculus comes from \(\frac{1}{|12|}\) so suppose that only one nucleotide was covered by the protein-DNA alignment

Lophocereus_schottii#

  • #TODO prefer transforming the links into contigs, and add new links between, change the sequences

  • Remove link \((10_f, 3_f)\)

Pelargonium_nanum#

  • Just raise the multiplicity of contig \(2\) from \(3\) to \(4\)

    • As \(4_{cov} = 67\), \(2_{cov} = 172\), and the minimum is \(6_{cov} = 56\): so because \(172 / 56 = 3.07\), the multiplicity of contig \(2\) will not become \(4\) even if we take as the starter the contig with the minimum coverage

Podocarpus_totara#

  • Remove link \((6_f, 11_r)\)

Triosteum_pinnatifidum#

  • \(7_{prob} \gets 0.01\)