User: Tospohh

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Tospohh10
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10
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1 week, 5 days ago
Joined:
8 years, 5 months ago
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f**@sanger.ac.uk

Posts by Tospohh

<prev • 5 results • page 1 of 1 • next >
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Comment: C: Problem with memory requirements for SPades
... Thanks! Wasn't aware of that tool either, will try it out! ...
written 5 weeks ago by Tospohh10
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Comment: C: Problem with memory requirements for SPades
... I tried various settings for -m but whatever I use, it always tries to use more than is available. And of course the above command was run on a machine that did have 250GB RAM but it ended up requesting almost 380GB despite -m being 250 by default. Max k was (automatically) set to 77 ...
written 5 weeks ago by Tospohh10
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Comment: C: Problem with memory requirements for SPades
... No, I wasn't aware of that. I haven't done a lot of assemblies and the last one was years ago. So from reading the manual you are referring to, I gather that I should aim for about 100x coverage. Is that a general recommendation or does it depend on the genome in question and the assembler? ...
written 5 weeks ago by Tospohh10
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Problem with memory requirements for SPades
... I am trying to assemble **Illumina MiSeq paired-end reads** from two **Plasmodium falciparum** samples. The genome is only about *20Mb* long. The two samples are quite **similar in the number of sequence reads** with both having about **900,000 read pairs**. I ran **SPades** on a machine with **250 ...
assembly spades written 5 weeks ago by Tospohh10
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Convert Lasergen Seqbuilder Project Files To Plain Text
... Is there any way of converting Lasergene SeqBuilder project files (*.sbd) into some plain text format like genbank? I only need the sequence and sequence features but I have a lot of sbd files and it would be great to do the whole batch with a script. Thanks! ...
format conversion written 8.5 years ago by Tospohh10 • updated 2.5 years ago by Biostar ♦♦ 20

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Popular Question 8.4 years ago, created a question with more than 1,000 views. For Convert Lasergen Seqbuilder Project Files To Plain Text

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