Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Aligning whole genome (FASTA) to reference genome

    Hello all,

    I previously aligned several fastq files (sample.merged.dedup.realn.bam) to a reference genome using bwa-mem.
    Now I want to align a different species sample to the same reference genome, but this file is a whole genome sequence in fasta format.

    I found this thread: http://seqanswers.com/forums/showthread.php?t=35608

    Which made me tempted to use bowtie2 like this:

    Code:
    bowtie2 -p 4 -f -x reference -U genome.fasta -S genome.aligned.sam
    However I'm not sure I can do this or if I should try using a different tool/method.
    After aligning and converting to bam format, I want to do variant calling for the whole dataset.

    Thank you in advance,
    Maria

  • #2
    I think it would be better to use minimap2 with the asm5 asm10 asm20 settings, see


    Preset:
    -x STR preset (always applied before other options; see minimap2.1 for details) []
    - map-pb/map-ont: PacBio/Nanopore vs reference mapping
    - ava-pb/ava-ont: PacBio/Nanopore read overlap
    - asm5/asm10/asm20: asm-to-ref mapping, for ~0.1/1/5% sequence divergence
    - splice: long-read spliced alignment
    - sr: genomic short-read mapping

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Latest Developments in Precision Medicine
      by seqadmin



      Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

      Somatic Genomics
      “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
      05-24-2024, 01:16 PM
    • seqadmin
      Recent Advances in Sequencing Analysis Tools
      by seqadmin


      The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
      05-06-2024, 07:48 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 05-24-2024, 07:15 AM
    0 responses
    15 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-23-2024, 10:28 AM
    0 responses
    18 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-23-2024, 07:35 AM
    0 responses
    21 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-22-2024, 02:06 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Working...
    X