Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Alignment Visualization

    I am looking for a way to align contigs from a de novo assembly against a reference genome and visualize which parts of the genome are covered. Any recommendations?

    Thanks

  • #2
    I really like Tablet (http://bioinformatics.oxfordjournals...t/btp666v1.pdf) as a genome viewer. I believe it supports ACE, AFG, MAQ, SOAP and SAM formats.

    Comment


    • #3
      But Tablet is for viewing individual contigs from assemblies on their own (looking at the reads within a contig).

      The question was about comparing the contigs of an assembly against a reference genome. This has similarities to comparing different genomes... maybe ACT (the Artemis Comparison Tool) would be suitable?
      Wellcome Sanger Institute tools directory

      Comment


      • #4
        We used BLASTn to map ca 2000 contigs against various references.
        Visualisation of contig position and the annotated genes in that region was with the R package GenomeGraphs.

        I would really recommend this and can send an example script if you pm me with your email address.

        Comment


        • #5
          What is your average contig length? For contigs assembled from short reads I have been using " bwa bwasw"

          It natively produces SAM format which your can convert to BAM and directly view in Tablet/IGV

          Comment


          • #6
            mummer may be best option

            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...
              Yesterday, 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, 04-11-2024, 12:08 PM
            0 responses
            58 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-10-2024, 10:19 PM
            0 responses
            53 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-10-2024, 09:21 AM
            0 responses
            45 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-04-2024, 09:00 AM
            0 responses
            55 views
            0 likes
            Last Post seqadmin  
            Working...
            X