User: avismirabilis

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Posts by avismirabilis

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Minia assembler restart after error?
... Nothing unusual regarding setup. linux server (not cluster), 80 cores with 60 TB free space, and 512Gb RAM. I took you advice and ran the latest version of Minia- actually using the GATB pipeline. That one completed through all K's within 48 hours. Strange phenomenon was that i got better assembly ...
written 9 months ago by avismirabilis40
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Comment: C: Minia assembler restart after error?
... The genome is a of a Crane species - approx 1.3Gb expected genome size. We have about 800 million reads, so I was wondering if that was the reason for how long it was taking. ...
written 9 months ago by avismirabilis40
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Minia assembler restart after error?
... My genome assembly was running fine with 22% completed on the 'Assembly' step. It had already taken 72 hours to get here. My system had to be shutdown for some critical security updates, and I had to interrupt the Minia run. Anyway to re-start from where I aborted, or back to square one? ...
assembly minia written 10 months ago by avismirabilis40 • updated 10 months ago by Rayan Chikhi1.4k
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Comment: A: The Biostar Handbook, a bioinformatics e-book for beginners
... Congratulations @Istvan. About to buy the handbook. Looking forward to having this on my desktop! ...
written 2.0 years ago by avismirabilis40
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Replicates in microbiota analyses: Pool sequences or average counts?
... I cannot really find a good answer to this question anywhere (eg. in the manuals of microbiota analysis software): Let say I have a study comparing the microbiota of two treatment groups. I have 5 replicates for each treatment group. Other than performing ANOVA type analyses where you can define tre ...
microbiome replication written 2.1 years ago by avismirabilis40 • updated 23 months ago by Biostar ♦♦ 20
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Variant calling and linkage disequilibrium when using de novo assembles
... I am working with a de novo genome assembly with thousands of scaffolds. This assembly is not close to have some of the scaffolds localized to chromosomes. One of the problems I have noticed is that two SNPs that are next to each other on a scaffold, for example, are not actually from the same chrom ...
linkage assembly snp assembly-quality ld written 2.1 years ago by avismirabilis40
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Comment: C: Pat Schloss of Mothur uses this
... Its been on and off for a few days. I was able to access wiki once on Friday, and mostly off otherwise ...
written 2.1 years ago by avismirabilis40

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Commentator 24 months ago, created a comment with at least 3 up-votes. For A: The Biostar Handbook, a bioinformatics e-book for beginners

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