Discussions

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  Question about the use of --trusted-contigs feature in Spades

  Subhajeet1997 asked Sep 12, 2024 in Q&A · Closed · Unanswered

  

  

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  [QUESTION] Best practice for input of PacBio IsoSeq data into hybrid rnaSPAdes

  martsper asked Apr 14, 2021 in Q&A · Unanswered

  

  

  

  

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  Regarding application of TP:Z:circular flag

  StamatisUCR asked Aug 19, 2024 in Q&A · Unanswered

  

  

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  When should we use Metaviral-spades instead of Meta-spades, given that it is designed for complete genomes?

  actledge asked Nov 7, 2023 in Q&A · Unanswered

  

  

  

  

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  How SPAdes prevents self-loops while breaking sequences into even-sized words?

  apcamargo asked Aug 13, 2024 in Q&A · Closed · Answered

  

  

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  k-mer coverage computation

  apcamargo asked Aug 12, 2024 in Q&A · Closed · Answered

  

  

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  What's the best practice for locating a gene in SPAdes assembly graph?

  nettanetta asked Jul 22, 2024 in Q&A · Unanswered

  

  

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  Automatic resolution of repeat regions in bacterial genome hybrid assembly (isolate)

  felince asked Jul 18, 2024 in Q&A · Unanswered

  

  

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  Recommendation for metagenomic assembly when only single-end data are available

  charlesfoster asked Jul 15, 2024 in Q&A · Answered

  

  

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  Creating a Continuous Contig from SPAde Output

  Abrar-co asked Jul 5, 2024 in Q&A · Closed · Unanswered

  

  

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  --isolate or --careful, what should I choose?

  m-rq asked Feb 4, 2023 in Q&A · Unanswered

  

  

  

  

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  Which graph file to use?

  felince asked Jun 25, 2024 in Q&A · Unanswered

  

  

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  Combined Illumina libraries of different length

  Phismil asked Dec 17, 2022 in Q&A · Unanswered

  

  

  

  

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  Compile SPAdes with Intel oneapi?

  inDane asked Jun 18, 2024 in Q&A · Unanswered

  

  

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  recompile with a larger setting for MI_HEAP_REGION_MAX_SIZE

  bowmanjeffs asked May 26, 2024 in Q&A · Closed · Unanswered

  

  

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  Error -9 assembly short reads

  Giulica13 asked May 20, 2024 in Q&A · Unanswered

  

  

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  How to use -- trust config module correctly?

  zhanchunhui asked Apr 25, 2024 in Q&A · Closed · Answered

  

  

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  Error, system call for...

  oom Out of memory log Errors explained in the log file

  Sunshaoe asked Apr 20, 2024 in Q&A · Closed · Unanswered

  

  

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  Mitochondrial assembly

  HNTHUS asked Apr 18, 2024 in Q&A · Closed · Unanswered

  

  

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  Merge contigs (chromosome and plasmid) from two assemblers

  cjp931401 asked Apr 4, 2024 in Q&A · Unanswered

  

  

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  After upgrading to python3.12 : Error importing LooseVersion from distutils. Now needs to come directly from looseversion.

  haslamdb started Mar 26, 2024 in General · Closed

  

  

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  Some contig sequences are not supported well by read mapping in a very low-depth metagenome assembly.

  ilnamkang asked Mar 12, 2024 in Q&A · Unanswered

  

  

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  Questions on Co-assembly with metaSPAdes for Metagenomic Analysis

  Pompamm asked Mar 1, 2024 in Q&A · Closed · Unanswered

  

  

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  == Error == system call OS return value: -9

  andrewisaiah asked Feb 21, 2024 in Q&A · Closed · Unanswered

  

  

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  Error correction and assembling warnings

  liuyca1 asked Feb 18, 2024 in Q&A · Closed · Unanswered

  

  

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