User: bioinfo

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bioinfo740
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Posts by bioinfo

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Metagenomics vs metatranscriptomics
... Hi all, This is more of a st of "technical questions" from biology and computational science but still part of bioinformatics issues to select right approaches at the beginning of your project. (1) I want to get an overall "microbial community" picture including bacteria, viruses (both DNA and ...
metatranscriptomics assembly metagenomics rna-seq written 4 weeks ago by bioinfo740 • updated 4 weeks ago by Mensur Dlakic1.7k
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Comment: C: Assembling multipartite (e.g. tripartite) viruses
... Yes, "tripartite" refers to 3 different segments that the virus made of. I will look into Brian's BBMap suite. Thanks. ...
written 7 weeks ago by bioinfo740
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Assembling multipartite (e.g. tripartite - 3 segments) viruses
... Hi all, I have sequenced (whole genome sequencing) a few isolates of a tripartite virus on MiSeq. I have done some preliminary assembly using SPAdes. I'm planning to obtain the "complete" genome for these isolates and make a comparative analysis. Since it is a tripartite genome how can I handle tha ...
assembly virus written 7 weeks ago by bioinfo740
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Comment: C: Downloading all COI sequences from BOLD database
... I am thinking the API solution such as below will do the job. I'm testing it now. wget http://v3.boldsystems.org/index.php/API_Public/sequence?marker=COI-5P More info are available here about API http://v3.boldsystems.org/index.php/resources/api?type=webservices#sequenceParameters ...
written 8 weeks ago by bioinfo740
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Comment: C: Downloading all COI sequences from BOLD database
... It seems the TSV file contains only a set of plant sequences (rbcL and some matK, n=1900 sequences) from 2015 release. ...
written 8 weeks ago by bioinfo740
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Downloading all COI sequences from BOLD database
... Hi all, Is there a way to download all `COI` sequences from `BOLD database` (http://www.boldsystems.org/index.php/Public_SearchTerms)? I tried to download all sequences from the search button of "Public Data Portal" without any search term but it returns zero hits. I also tried with a search term ...
bold coi barcoding written 8 weeks ago by bioinfo740
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Comment: C: Senior bioinformatician, Auckland, New Zealand (3 yrs fixed-term)
... Yes, anyone can apply. Applicants from outside of New Zealand and Australia can apply for a work visa with our sponsorship/appointment letter, once selected. ...
written 11 weeks ago by bioinfo740
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Job: Senior bioinformatician, Auckland, New Zealand (3 yrs fixed-term)
... **Senior Scientist - Bioinformatics** **Auckland, New Zealand** The Ministry for Primary Industries' Plant Health & Environment Laboratory (PHEL) in Auckland has a fixed-term vacancy (36 months) for a senior bioinformatician to work on a project to develop a bioinformatics toolkit for the dete ...
software database sequencing job virus written 11 weeks ago by bioinfo740
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Forum: NGS Data storage solutions for small organisations or big labs
... Hi all, I’m trying to find out and compile info on how big labs (e.g. 40+ people) or small organisations who produce large amounts of NGS data manage the data storage issue. As a small organisation, we produce 10-15 TBs of HTS data every year from large genomics and metagenomics projects. We are o ...
forum ngs storage bigdata metagenomics hts written 4 months ago by bioinfo740 • updated 3 months ago by i.sudbery5.9k
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Required packages during Cygwin installation for bioinformatics work
... Hi, many of us install Cygwin in our windows machine to have the Linux like feel. In default, many packages don't get installed when we install Cygwin. And, as a consequence, many simple commands don't work. For example, wget (https://superuser.com/questions/693284/wget-command-not-working-in-cygwin ...
wget cygwin tools written 6 months ago by bioinfo740 • updated 3 months ago by colindaven1.7k

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