User: lotus28

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lotus2860
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Posts by lotus28

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Comment: C: Host Decontamination: bbTools or Samtools?
... Yes, probably tweaking bbTools pipeline might work, but I have not noticed any significant gain in speed to justify this tweaking. For the time being I will just stick with my current pipeline. ...
written 4 months ago by lotus2860
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Comment: C: Host Decontamination: bbTools or Samtools?
... Yesterday I ran some tests to compare bowtie2 and bbTools decontamination. I used the same index provided in your link for both. bbTools takes longer to compute (15-30% longer) and deletes fewer reads. It also seems like bbTools has lower sensitivity, even in heavily contaminated runs. I think I wil ...
written 4 months ago by lotus2860
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Comment: C: Host Decontamination: bbTools or Samtools?
... Basic samtools stuff: align against hg19 with bowtie2, extract reads with both ends unmatched, sort and convert filtered bams to fastq. I was just wondering if I could remove one docker container from my pipeline by using bbTools for both quality trimming and decontamination ...
written 4 months ago by lotus2860
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Host Decontamination: bbTools or Samtools?
... Hi, I have always used Samtools to remove any human contaminants from my gut flora data. However, bbTools also allows you to do that. All the post I've seen mention using bbTools for small contaminants removal. Is it practical to use it for removing hg19 contaminants or should I stick with Bowtie + ...
metagenomics quality control decontamination written 4 months ago by lotus2860 • updated 4 months ago by genomax74k
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Functional Metagenomic Analysis Tools
... I am going to perform functional analysis on a large collection of WGS gut metagenomes. However, options are too numerous. There is MEGAN6, MOCAT2, others. For me resource efficiency is key. I have discovered [SUPER-FOCUS][1], that is claimed to be super-fast, but the lack of updates keeps me worrie ...
microbiome metagenomics protein function written 8 months ago by lotus2860
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Comment: C: Metagenomics best reference DB
... That's great news I am not sure that it counts as behind schedule. The announcement is from April 2018 and says that from Fall 2018 onwards SILVA will be free for all purposes. So, I believe that Silva is now free for commercial use. ...
written 10 months ago by lotus2860
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Comment: C: Metagenomics best reference DB
... That's interesting. Are you aware of any qiime2 compatible classifiers for RDP? ...
written 10 months ago by lotus2860
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Comment: C: Metagenomics best reference DB
... But RDP does not report taxa names below genus, does it? That is what I'd like the most from a ref DB, as I intend to use 16S as a "crutch" for my WGS study. ...
written 10 months ago by lotus2860
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Metagenomics best reference DB
... I cannot decide which reference I should use to map my gut microbiome 16S data. Greengenes seems to be the best choice, but last time it was updated in 2013 and metagenomics has moved far ahead since then. Won't I be missing a huge part of biodiversity, if I use it? Also, this [article][1] keeps me ...
greengenes metagenomics silva 16s written 10 months ago by lotus2860
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Gut microbe annotation DB
... As a result of my study I have received a number of bacterial species that are important for developing a medical condition. Now I would like to know, what are these bacteria's role in gut microbiome. I want to see which of them have invasive potential, what metabolites they feed on and what they p ...
gut microbiome bacteria ecology microbiology written 13 months ago by lotus2860 • updated 12 months ago by Dattatray Mongad340

Latest awards to lotus28

Supporter 4 months ago, voted at least 25 times.
Popular Question 9 months ago, created a question with more than 1,000 views. For What are RMA units?
Student 9 months ago, asked a question with at least 3 up-votes. For Metagenomics best reference DB
Popular Question 13 months ago, created a question with more than 1,000 views. For What are RMA units?
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