User: alslonik

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alslonik20
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New User
Location:
Israel
Last seen:
3 days, 19 hours ago
Joined:
1 year, 1 month ago
Email:
a*******@gmail.com

ARO, Voulkani research center

Posts by alslonik

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Falcon - Estimation of free disc space needed
... Also, just in case someone needs - here are most of the answers to my questions : https://github.com/PacificBiosciences/FALCON/wiki/Somethings-to-think-about-for-tuning-assembly-parameters Important text for newbies like me assembling de novo for the first time. ...
written 3 days ago by alslonik20
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Answer: A: Falcon - Estimation of free disc space needed
... OK, So I am answering to myself just in case someone who reads it will need it. It is abnormal to have these sizes and these numbers of jobs with Falcon trying to assemble a less than 1G genome with a 120X coverage. A **Dbsplit** option in the cfg file that takes care of the block size at the dealig ...
written 5 days ago by alslonik20
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Comment: C: Falcon - Estimation of free disc space needed
... Thanks, Falcon does some internal filtering at the beginning, but yes - I guess you are right, and if there will no be additional option I will filter the reads! I ll look deeper into these settings parameters...Thank you! ...
written 8 days ago by alslonik20
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Falcon - Estimation of free disc space needed
... Hi, I am running a de novo assembly of a plant ~500Mb genome from PacBio reads of 120X coverage with Falcon. It runs for about 5 days now, done ~20% of the 160000 jobs that it has, and the disc space it takes is 2.5T currently. My free disc is up to 6T, meaning that I have 3.5T free. I am trying to ...
assembly falcon pacbio written 9 days ago by alslonik20
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SPADES - STAGE == Distance Estimation. resolvable_repeat_length_bound set to 10000. Shows no signs of life in log for 12h.
... People that have experience with SPAdes, is it a normal stage that is just time-consuming or maybe something is stuck and abnormal? Id does not show any sign that smth is happening. The script is running on one core only (It is set to run on 24 originally). It showed very detailed log for about eve ...
assembly written 11 days ago by alslonik20
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Answer: A: How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
... We also use BUSCO (https://busco.ezlab.org/), along with QUAST, already mentioned and statistics as size of scaffolds, percentage of gaps, N50 etc. ...
written 18 days ago by alslonik20
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Comment: C: De novo plant genome assembly
... Thanks. Re: 10x assembly: it is ~200Mb size after ordering with ALLMAPs which is 2/3 of the expected size. BUSCO shows 88% complete plant BUSCOs. Illumina repeats were never successfully assembled. I actually am thinking of doing it now. ...
written 20 days ago by alslonik20
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De novo plant genome assembly
... Hello clever community! I need your advice. I am working on a *de novo* plant genome assembly of ~400 Mb. I have Chromium 10x data, which was assembled with supernova. I also have Illumina paired end reads. Now I have additional data of PacBio reads, 120x roughly. The genome is diploid and I am th ...
genome assembly chromium falcon pacbio written 20 days ago by alslonik20
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Comment: C: Need help running HGAP4 on polymorphic genome
... It runs more than one week. Around 7 days and 10 h. ...
written 21 days ago by alslonik20
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Comment: C: Need help running HGAP4 on polymorphic genome
... Hi, re: BUSCO. I am working on plant genomes and 35 missing seems a fairly good result in terms of percentage. What is you total Complete BUSCOs in %? Maybe the assembly you get is not that bad? I am also curious about the time that it took to run the assembly with Falcon. I am trying to assemble n ...
written 24 days ago by alslonik20

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Scholar 5 days ago, created an answer that has been accepted. For A: Falcon - Estimation of free disc space needed

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