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Skip to primary content. Skip to secondary content. Does NP-completeness have a role to play in Bioinformatics? June 22, 2016. This paper just came out a few days ago: Read mapping on de Bruijn graphs. Papers come and papers go, I didn’t think more of it until recently on twitter. The paper is bogus and the problem is certainly not NP-complete. See e.g. hybridSPAdes paper, it describes read-to-graph alignment. Mdash; SPAdes assembler (@spadesassembler) June 21, 2016. There is a similar formulation for th...

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Bits of Bioinformatics | pmelsted.wordpress.com Reviews

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Skip to primary content. Skip to secondary content. Does NP-completeness have a role to play in Bioinformatics? June 22, 2016. This paper just came out a few days ago: Read mapping on de Bruijn graphs. Papers come and papers go, I didn’t think more of it until recently on twitter. The paper is bogus and the problem is certainly not NP-complete. See e.g. hybridSPAdes paper, it describes read-to-graph alignment. Mdash; SPAdes assembler (@spadesassembler) June 21, 2016. There is a similar formulation for th...

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Bits of Bioinformatics | pmelsted.wordpress.com Reviews

https://pmelsted.wordpress.com

Skip to primary content. Skip to secondary content. Does NP-completeness have a role to play in Bioinformatics? June 22, 2016. This paper just came out a few days ago: Read mapping on de Bruijn graphs. Papers come and papers go, I didn’t think more of it until recently on twitter. The paper is bogus and the problem is certainly not NP-complete. See e.g. hybridSPAdes paper, it describes read-to-graph alignment. Mdash; SPAdes assembler (@spadesassembler) June 21, 2016. There is a similar formulation for th...

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Skip to primary content. Skip to secondary content. Newer posts →. Naive python implementation of a de Bruijn Graph. November 23, 2013. De Bruijn graphs are widely used in assembly algorithms and I guess writing your own assembler is a rite of passage. Hoping to get some answers I got this question from Mick Watson. Since I had a script lying around that I used for validation I thought I would share it. Pall Melsted (@pmelsted) November 23, 2013. For x in fw(ATAT): print x. To keep track of all the k-mer...

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November | 2013 | Bits of Bioinformatics

https://pmelsted.wordpress.com/2013/11

Skip to primary content. Skip to secondary content. Monthly Archives: November 2013. Naive python implementation of a de Bruijn Graph. November 23, 2013. De Bruijn graphs are widely used in assembly algorithms and I guess writing your own assembler is a rite of passage. Hoping to get some answers I got this question from Mick Watson. Since I had a script lying around that I used for validation I thought I would share it. Pall Melsted (@pmelsted) November 23, 2013. For x in fw(ATAT): print x. To keep trac...

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October | 2015 | Bits of Bioinformatics

https://pmelsted.wordpress.com/2015/10

Skip to primary content. Skip to secondary content. Monthly Archives: October 2015. Building Binaries for Bioinformatics. October 14, 2015. Tl;dr there is a recipe for compiling binaries at the end. I run a cluster which runs on the rocks cluster system. The newest version at the time was based on Centos6, the compiler was gcc 4.4, even old at the time. The reason is that distributions are reluctant to use the latest compilers and so users are stuck with old technologies. How bad can it be? Linux is wond...

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February | 2014 | Bits of Bioinformatics

https://pmelsted.wordpress.com/2014/02

Skip to primary content. Skip to secondary content. Monthly Archives: February 2014. DeBuGging de Bruijn Graphs. February 24, 2014. In the previous posts I showed a toy implementation of a dBG assembler. And then found that something was wrong with the edge cases. I’ll show how to fix these edge cases by testing this on circular contigs and something similar. When we feed this to the assembler we get (I put cyclic.fq twice since by default I’m filtering k-mers with a coverage of 1). A) in the function.

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January | 2014 | Bits of Bioinformatics

https://pmelsted.wordpress.com/2014/01

Skip to primary content. Skip to secondary content. Monthly Archives: January 2014. Edge cases in de Bruijn graphs. January 17, 2014. In the previous post. I showed a simple implementation of a de Bruijn graph assembler. This implementation is mostly correct, for some definition of mostly. One of the key differences between the original combinatorial definition. Of a de Bruijn graph and what we use for assembly is that a) the. Edge then we must have a. The downside is the memory usage is doubled. Sin...

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Nicholas Wade’s troublesome inheritance | Bits of DNA

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Reviews and commentary on computational biology by Lior Pachter. Nicholas Wade’s troublesome inheritance. June 4, 2014 in guest post. Tags: A Troublesome Inheritance. There has recently been something of an uproar over the new book. By Nicholas Wade, with much of the criticism centering on Wade’s claim that race is a meaningful biological category. This subject is one with which I. 10 A simple pair of digits that conferred on me numerous rights and privileges denied to the majority of the population.

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Bits of Bioinformatics

Skip to primary content. Skip to secondary content. Does NP-completeness have a role to play in Bioinformatics? June 22, 2016. This paper just came out a few days ago: Read mapping on de Bruijn graphs. Papers come and papers go, I didn’t think more of it until recently on twitter. The paper is bogus and the problem is certainly not NP-complete. See e.g. hybridSPAdes paper, it describes read-to-graph alignment. Mdash; SPAdes assembler (@spadesassembler) June 21, 2016. There is a similar formulation for th...

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