Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • gsAssembler - predicted genome size?

    Hello a I have a quick question concerning "newbler" gsassembler(v2.3). Can anyone suggest how to find the predicted genome size from the output of a de novo assembly?

    To calc the n50 stat the predicted genome size is required, so I assume its there somewhere...

    Thanks in advance,

    Jordy

  • #2
    Hi Jordy,

    Look in the "454NewblerMetrics.txt" file. It lists the estimated genome size as well as the N50 Contig size (but I'm not sure if this is for all contigs or only large contigs).

    Comment


    • #3
      Originally posted by Jordy224 View Post
      To calc the n50 stat the predicted genome size is required, so I assume its there somewhere...Jordy
      Interesting that you write this, because the N50 definition variably is relative to estimated genome size, reference genome size (for reference assisted assembly/mapping) OR total assembled size. It is the last definition newbler uses: smallest contig size such that half the assembled bases are in contigs of at least that size.

      Obviously, the N50 size is also dependent on the minimum contig length included in the total, which in case of newbler is 500 bp.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Essential Discoveries and Tools in Epitranscriptomics
        by seqadmin




        The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
        04-22-2024, 07:01 AM
      • seqadmin
        Current Approaches to Protein Sequencing
        by seqadmin


        Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
        04-04-2024, 04:25 PM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 08:47 AM
      0 responses
      12 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-11-2024, 12:08 PM
      0 responses
      60 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 10:19 PM
      0 responses
      59 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 09:21 AM
      0 responses
      54 views
      0 likes
      Last Post seqadmin  
      Working...
      X