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  • 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

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