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#
\(7_{prob} \gets 0.01\)