Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • El Crazy Xabi
    replied
    Any update on this?

    Leave a comment:


  • GenoMax
    replied
    Originally posted by ronaldrcutler View Post
    Yes this is exactly what I'm looking for since doing assemblies in other programs with a larger size yields better contigs and kmer size predictors also indicate that a high kmer should be at least tried.
    Current limit is 127 with SPAdes unless you have programmatic chops to look in the source code to see if that can be changed.

    You can email SPAdes support with this question: spades.support at bioinf.spbau.ru

    Post their solution/answer here if you hear back.

    Leave a comment:


  • ronaldrcutler
    replied
    Originally posted by GenoMax View Post
    @ronaldrcutler wants to know (based on other threads posted here and on Biostars) if a value of more than 127 can be used in some way (clearly the software currently is limited at that level)?
    Yes this is exactly what I'm looking for since doing assemblies in other programs with a larger size yields better contigs and kmer size predictors also indicate that a high kmer should be at least tried.

    Leave a comment:


  • Andrei D.
    replied
    No, I'm basically wet biologist from another group and don't know answer to this question.

    Leave a comment:


  • GenoMax
    replied
    Originally posted by Andrei D. View Post
    You may specify the length of the kmers by adding " -k <int,int,...> " to default query "spades.py [options] -o <output_dir>".

    There is written in the manual:
    " Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128 and listed in ascending order). "
    @ronaldrcutler wants to know (based on other threads posted here and on Biostars) if a value of more than 127 can be used in some way (clearly the software currently is limited at that level)?

    Are you from the group that developed SPAdes? If yes then can you provide an answer for that.

    Leave a comment:


  • Andrei D.
    replied
    You may specify the length of the kmers by adding " -k <int,int,...> " to default query "spades.py [options] -o <output_dir>".

    There is written in the manual:
    " Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128 and listed in ascending order). "

    Leave a comment:


  • ronaldrcutler
    replied
    Bump

    I am facing the same issue as well and would like to know how to do this. Would it be similar to the way we increase it on velvet?

    Leave a comment:


  • Increasing the length of the kmers od Spades beyond 127

    Hi,
    is there a way to increase the length of the kmers used by spades 3.5 beyond 127? Because I tried different kmers and I saw that the quality of the assembly is better with longer kmers.
    My reads are pretty long so I think it shouldn't be a problem to use bigger kmers.
    I have not much experience with spades, or with bioinformatics in general, so I hope my question is not woefully stupid.
    Thanks to everyone for the future answers

Latest Articles

Collapse

  • seqadmin
    The Impact of AI in Genomic Medicine
    by seqadmin



    Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
    Yesterday, 02:07 PM
  • seqadmin
    Multiomics Techniques Advancing Disease Research
    by seqadmin


    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

    A major leap in the field has
    ...
    02-08-2024, 06:33 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 02-23-2024, 04:11 PM
0 responses
48 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-21-2024, 08:52 AM
0 responses
61 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-20-2024, 08:57 AM
0 responses
51 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-14-2024, 09:19 AM
0 responses
65 views
0 likes
Last Post seqadmin  
Working...
X