https://github.com/sjackman/scaffolding-coverage

Determine the required mate-pair coverage for scaffolding
https://github.com/sjackman/scaffolding-coverage

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Determine the required mate-pair coverage for scaffolding

• Host: GitHub
• URL: https://github.com/sjackman/scaffolding-coverage
• Owner: sjackman
• Created: 2015-07-07T16:21:49.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2015-07-07T16:21:56.000Z (over 9 years ago)
• Last Synced: 2024-10-13T20:46:43.267Z (2 months ago)
• Language: Makefile
• Size: 93.8 KB
• Stars: 1
• Watchers: 3
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
Determine the required mate-pair coverage for scaffolding

================================================================================

Determine the coverage in mate-pair libraries necessary for

scaffolding.

Tony wrote...

> Here are the alignments:

> /projects/ABySS/assemblies/PG/genome/abyss-1.3.4/PG29/20121204/k109/transcriptome_scaff/no-complex/w_mp40k/mp40k.sam

>

> They were aligned to the transcriptome rescaffolded assembly:

> /projects/ABySS/assemblies/PG/genome/abyss-1.3.4/PG29/20121204/k109/transcriptome_scaff/no-complex/w_mp40k/PG29-10.fa

Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler

Daniel R. Zerbino, Gayle K. McEwen, Elliott H. Margulies, Ewan Birney

http://dx.doi.org/doi:10.1371/journal.pone.0008407.g002

## Estimating the expected number of paired-end connections between two contigs

> For each pair of contigs connected by read pairs, and for each

> insert library, we call A the length of the longer node, B the

> length of the shorter one, D the estimated distance between the two,

> and ρ the density of paired-end reads on the longer node. The

> paired-end reads are characterised by the mean μ and the standard

> deviation σ of the insert length distribution.

>

> We first define a few variables:

>

> ![variables](http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0008407.e001&representation=PNG)

>

> We finally obtain an estimate of the expected number X of paired-end

> connections between the two contigs (cf. Text S1), using the

> probability density Q and the standard error function erf associated

> to the normal distribution:

>

> ![estimate](http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0008407.e002&representation=PNG)