Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • how to do reference based de novo assembly using velvet

    As above.

    Currently need to do a de novo assembly, but don't know how to use a reference in the velveth. : |


    Thanks for your reply!
    Last edited by arkilis; 12-01-2013, 11:01 PM.

  • #2
    I got some tips after google.

    velveth run 31 -reference PHAC_sample_2.txt -shortPaired -fastq.gz 1_001.fastq.gz 2_001.fastq.gz &
    But always got some error like:

    Incomplete Sequences file (computeHSPScores)
    Does anyone got any idea on this? Thanks a lot!

    Comment


    • #3
      I haven't seen that error message before,

      but usually when running velveth either you interleave the files containing R1 and R2, or you specify -separate if the R1 and R2 reads are in separate files.

      Comment


      • #4
        Google for "Velvet Columbus", which is the reference-guided de novo assembly pipeline.

        (Though on the off-chance you get weird results)

        Comment


        • #5
          Originally posted by arkilis View Post
          Currently need to do a de novo assembly, but don't know how to use a reference in the velveth.
          Then you should probably read the Columbus_manual.pdf which is included in the velvet distribution tar file.

          Basically you're doing it wrong. To do reference guided assembly in velvet you first align your reads to the reference with something like bowtie or bwa and then input the aligned read file (SAM) along with the reference file (FASTA) to velveth. You can not go directly from reads to reference guided assembly with velvet, prealignment is required.

          Comment


          • #6
            Originally posted by ctseto View Post
            Google for "Velvet Columbus", which is the reference-guided de novo assembly pipeline.

            (Though on the off-chance you get weird results)

            http://bioweb2.pasteur.fr/docs/velve...bus_manual.pdf
            Thanks for your advices.

            Comment


            • #7
              Originally posted by kmcarr View Post
              Then you should probably read the Columbus_manual.pdf which is included in the velvet distribution tar file.

              Basically you're doing it wrong. To do reference guided assembly in velvet you first align your reads to the reference with something like bowtie or bwa and then input the aligned read file (SAM) along with the reference file (FASTA) to velveth. You can not go directly from reads to reference guided assembly with velvet, prealignment is required.
              Hi I found out that if I use the -separate option, that will be fine. No such error anymore. But the N50 is pertty lame (only 100, kmer 103). I read the http://bioweb2.pasteur.fr/docs/velve...bus_manual.pdf you mentioned, but there is no clue on do alignment before velvet assembly. Why you suggest to do that? thx

              Comment


              • #8
                Originally posted by arkilis View Post
                I read the http://bioweb2.pasteur.fr/docs/velve...bus_manual.pdf you mentioned, but there is no clue on do alignment before velvet assembly. Why you suggest to do that? thx
                On page 2, section 3 "Overview of the process", step 1 says
                Map the reads against a set of target sequences (typically, an entire reference genome, made up of chromosomal sequences).
                Step 4 then says
                Provide this FASTA file along with the SAM/BAM alignment file
                ("this FASTA file means the reference file")

                Pretty clear indication that alignment is the first step and you input the reference and alignment, not the read fastq files.

                Comment


                • #9
                  Originally posted by kmcarr View Post
                  On page 2, section 3 "Overview of the process", step 1 says

                  Step 4 then says ("this FASTA file means the reference file")

                  Pretty clear indication that alignment is the first step and you input the reference and alignment, not the read fastq files.

                  Genius, I did not read the manual carefully. But when I run the velveth with columbus, I got:

                  "WARNING: None of your read mappings recognized the reference sequence!"

                  Is that mean I got the wrong reference file or does not recognized at all?
                  Last edited by arkilis; 12-04-2013, 09:55 PM.

                  Comment

                  Latest Articles

                  Collapse

                  • 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
                  • seqadmin
                    Strategies for Sequencing Challenging Samples
                    by seqadmin


                    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                    03-22-2024, 06:39 AM

                  ad_right_rmr

                  Collapse

                  News

                  Collapse

                  Topics Statistics Last Post
                  Started by seqadmin, 04-11-2024, 12:08 PM
                  0 responses
                  11 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 04-10-2024, 10:19 PM
                  0 responses
                  17 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 04-10-2024, 09:21 AM
                  0 responses
                  14 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 04-04-2024, 09:00 AM
                  0 responses
                  43 views
                  0 likes
                  Last Post seqadmin  
                  Working...
                  X