Title: The Basic Alignment Workflow  
Owner: Anna Battenhouse
Creator: Anna Battenhouse May 12, 2014
Last Changed by: Anna Battenhouse Jun 04, 2025
Tiny Link: (useful for email) https://cloud.wikis.utexas.edu/wiki/x/2QY5Aw
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Core NGS Tools (3)
    Home page: Core NGS Tools Home
    Page: Day 4: Alignment and BAM file manipulation
    Page: Filtering with SAMTools
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Jun 04, 2025 14:04 Anna Battenhouse View Changes
Jun 01, 2025 16:06 Anna Battenhouse View Changes
Jun 01, 2025 15:52 Anna Battenhouse View Changes
Jun 01, 2025 14:28 Anna Battenhouse View Changes
May 30, 2025 14:18 Anna Battenhouse  
Outgoing Links
External Links (14)
    https://cloud.wikis.utexas.edu/wiki/spaces/CbrsIntroUnix/pa…
    https://cloud.wikis.utexas.edu/wiki/spaces/CbrsIntroUnix/pa…
    blast.ncbi.nlm.nih.gov/Blast.cgi
    hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/
    en.wikipedia.org/wiki/Burrows-Wheeler_transform
    https://www.mirbase.org/download/
    samtools.sourceforge.net/
    perldoc.perl.org/perlretut.html
    bio-bwa.sourceforge.net/bwa.shtml
    hgdownload.cse.ucsc.edu/goldenPath/sacCer3/bigZips/
    genomewiki.ucsc.edu/index.php/Hg19_Genome_size_statistics
    https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_008369605.…
    en.wikipedia.org/wiki/Sequence_alignment_software
    https://samtools.github.io/hts-specs/SAMv1.pdf
Core NGS Tools (2)     Page: The Basic Alignment Workflow
    Page: Linux fundamentals