Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Compare Genomes

    Hi everyone, I did Genome assembly by SOAPdenovo and obtained contigs and scaffolds, now I wanna compare these scaffolds to some reference genomes downloaded from Genbank. I am wondering what tools I can use to do this job, I used BLAST but it is not in good visualization, any other advice on such tools and programs?
    I am new to this, any suggestion is appreciated.
    Thanks

  • #2
    Use NUCmer from the MUMmer package (available from Sourceforge.) For large reference genomes, you have to split the reference into smaller pieces for it to fit in memory, then align everything to those pieces. It is relatively fast and efficient, and seems to be a commonly used tool as the basis for other assembly comparison pipelines. There are some recently available wrapper scripts which automate some of the steps, but it's not tough to run through the steps yourself. The online docs for MUMmer as a whole are very good.

    Comment


    • #3
      For mammalian genomes, use bwa-sw. Two human assemblies in several CPU days.

      Comment


      • #4
        De novo to reference comparison

        I have had good luck with both MUMmer and MAUVE.
        MAUVE is very straight forward and MUMmer I simply follow the recipes in the manuel.

        Comment


        • #5
          But is it good to use the contigs files or to use the scaffolds files for comparison?

          Comment


          • #6
            Compare Genomes

            I suppose it depends what your question is.
            But, typically the goal of genome assembly is to create one scaffold per chromosome (assemble the entire genome/chromosome). With this in mind, I think it would make more sense to compare scaffolds to scaffolds.

            Comment


            • #7
              However, scaffolds are nothing but a combination of contigs filled with "estimates" of gaps in between. Does that not mean then that it is more sensible to compare contigs than to compare scaffolds as it has estimate of gaps in between which may be highly erroneous!

              Comment

              Latest Articles

              Collapse

              • seqadmin
                Exploring the Dynamics of the Tumor Microenvironment
                by seqadmin




                The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
                07-08-2024, 03:19 PM
              • seqadmin
                Exploring Human Diversity Through Large-Scale Omics
                by seqadmin


                In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
                06-25-2024, 06:43 AM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, Yesterday, 05:49 AM
              0 responses
              15 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 07-15-2024, 06:53 AM
              0 responses
              27 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 07-10-2024, 07:30 AM
              0 responses
              39 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 07-03-2024, 09:45 AM
              0 responses
              204 views
              0 likes
              Last Post seqadmin  
              Working...
              X