User: dbrowne.up

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dbrowne.up60
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Posts by dbrowne.up

<prev • 14 results • page 1 of 2 • next >
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Answer: A: optimum number of short reads for denovo assembly
... For a rough (and imperfect) estimation, use the formula: `C = R x L / G` Where C is coverage, R is total number of reads, L is read length, and G is genome size. So for a 15 kb genome, with 250 bp reads, in order to get 60X coverage, you need about 3,600 reads. ...
written 13 months ago by dbrowne.up60
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Answer: A: Denovo Assemly of unmapped reads
... In my experience, different regions of the genome are assembled optimally by different k-mer values. There is not one universally optimal k-mer value. ...
written 13 months ago by dbrowne.up60
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Answer: A: scoffold level assembly
... [BESST](https://github.com/ksahlin/BESST) is another scaffolder worth checking out. I personally like it a lot better than SSPACE. ...
written 13 months ago by dbrowne.up60
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Answer: A: estimate genome coverage
... Or more broadly and easily... `C = R x L / G` Where C is physical coverage, R is the total number of reads, L is (average) read length, and G is the genome size. So for example, if you have a 100 Mbp genome and an Illumina library with 10 M reads of length 150 bp, the coverage of the genome is 15X ...
written 13 months ago by dbrowne.up60
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Answer: A: how to assign kmer value for paired end reads
... Personally, I don't think that a single k-mer value will give you an optimal assembly. Different k-mer sizes will optimally assemble different regions of the genome. Since you're doing metagenomic assembly, check out this program called MeGAMerge: https://github.com/LANL-Bioinformatics/MeGAMerge It ...
written 13 months ago by dbrowne.up60
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Answer: A: How to find the longest common sequence for a cluster of sequences in a fasta fi
... Check out the Python module pyfaidx: https://github.com/mdshw5/pyfaidx It makes doing this sort of thing super easy. You may have to experiment a bit to figure out how to do exactly what you are wanting to, but with pyfaidx, you have a nice interface to access each sequence in your file and get inf ...
written 19 months ago by dbrowne.up60
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Answer: A: What are the cut-offs during read quality filtering in Bowtie/TopHat before mapp
... I am wondering the same thing about Bowtie2. I think it must include the Phred scores in the calculation of the Alignment Score and the corresponding MAPQ, considering that you can specify either --phred33 or --phred64. I haven't found a whole lot of resources explaining this, but this is what I've ...
written 20 months ago by dbrowne.up60
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Comment: C: Using ABySS Tools for Ad Hoc OLC Assembly
... Thanks Ben! Quick follow-up question: how are transitive edges and shims defined? Just wondering whether or not I should aim to filter those out of the overlap graph prior to layout and consensus. ...
written 20 months ago by dbrowne.up60
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Answer: A: good scaffolder tool !
... BESST, SSPACE, SOPRA, and OPERA are some commonly used scaffolding tools. See this paper for a more detailed analysis of scaffolding tools: http://www.genomebiology.com/2014/15/3/R42 ...
written 20 months ago by dbrowne.up60
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Using ABySS Tools for Ad Hoc OLC Assembly
... Hello, I have a set of contigs that I would like to re-assemble using an Overlap-Layout-Consensus (OLC)-type approach. Let's say the minimum contig size in the set is 1000 bp. If I understand correctly, the following commands should: 1) find all overlaps between 100-999 bp, and store that overlap i ...
assembly abyss written 20 months ago by dbrowne.up60 • updated 20 months ago by benv600

Latest awards to dbrowne.up

Supporter 13 months ago, voted at least 25 times.
Scholar 21 months ago, created an answer that has been accepted. For A: Using the ABySS pipeline to scaffold a DISCOVAR de novo assembly

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