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Title: Core NGS Resources  
Author: Anna M Battenhouse May 11, 2014
Last Changed by: Anna M Battenhouse Jun 08, 2021
Tiny Link: (useful for email) https://wikis.utexas.edu/x/wrb5Aw
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Core NGS Tools (1)
    Home page: Core NGS Tools Home
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    Page: Resources
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External Links (94)
    hannonlab.cshl.edu/fastx_toolkit/
    www.nature.com/nprot/journal/v11/n9/full/nprot.2016.095.htm…
    www.ncbi.nlm.nih.gov/Traces/sra/?view=software
    hannonlab.cshl.edu/fastx_toolkit/commandline.html
    https://github.com/lh3/bwa/blob/master/README-alt.md
    https://www.gencodegenes.org/
    genome.ucsc.edu
    https://github.com/alexdobin/STAR/releases
    https://wikis.utexas.edu/display/GSAF/Illumina+-+all+flavor…
    https://cutadapt.readthedocs.io/en/stable/
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/
    https://nanoporetech.com/
    genome.ucsc.edu/cgi-bin/hgTables
    www.ncbi.nlm.nih.gov/sra
    www.pacb.com/smrt-science/smrt-sequencing/
    lh3lh3.users.sourceforge.net/NGSalign.shtml
    samtools.github.io/hts-specs/
    https://www.youtube.com/watch?v=fCd6B5HRaZ8
    https://wikis.utexas.edu/display/bioiteam/Using+MultiQC
    bio-bwa.sourceforge.net/
    www.pacb.com/wp-content/uploads/Ekholm-ASHG-2016-Enrichment…
    https://software.broadinstitute.org/cancer/cga/rnaseqc_run
    hgdownload.cse.ucsc.edu/admin/exe/
    www.bioinformatics.babraham.ac.uk/projects/fastqc/
    korflab.ucdavis.edu/bootcamp.html
    www.hindawi.com/journals/bmri/2012/251364/
    www.htslib.org/
    bejerano.stanford.edu/great/public/html/splash.php
    https://david.ncifcrf.gov/
    cbl-gorilla.cs.technion.ac.il/
    ccb.jhu.edu/software/tophat/index.shtml
    seqanswers.com/forums/showthread.php?t=4589
    https://github.com/samtools/hts-specs/blob/master/SAMtags.p…
    hgwdev.cse.ucsc.edu/FAQ/FAQformat.html#format1
    https://github.com/alexdobin/STAR/blob/master/doc/STARmanua…
    multiqc.info/
    hgdownload.cse.ucsc.edu/downloads.html
    https://www.bioconductor.org/help/workflows/rnaseqGene/
    hgwdev.cse.ucsc.edu/
    geneontology.org/
    https://www.internationalgenome.org/data-portal/sample
    https://github.com/lh3/seqtk
    en.wikipedia.org/wiki/FASTQ_format
    meme-suite.org/
    korflab.ucdavis.edu/Unix_and_Perl/unix_and_perl_v2.3.4.pdf
    www.broadinstitute.org/software/igv/download
    https://bioconductor.org/packages/release/bioc/vignettes/DE…
    usegalaxy.org/
    bedtools.readthedocs.io/en/latest/content/bedtools-suite.ht…
    broadinstitute.github.io/picard/command-line-overview.html#…
    www.youtube.com/watch?v=77r5p8IBwJk
    https://software.broadinstitute.org/gatk/documentation/arti…
    ftp.ensembl.org/pub
    www.youtube.com/watch?v=bFNjxKHP8Jc
    https://www.ncbi.nlm.nih.gov/refseq/
    bioinfo.single-cell.cn/rna-qc-chain.html
    https://ccb.jhu.edu/software/hisat2/index.shtml
    https://utexas.zoom.us/rec/share/x1zCXQg-nB1HZYzgnXb8VK44J0…
    https://utexas.zoom.us/rec/play/5co1OfvhN5650hOccTNzANod0hU…
    samtools.sourceforge.net/
    https://pachterlab.github.io/kallisto/
    https://software.broadinstitute.org/cancer/cga/rna-seqc
    www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html
    https://aws.amazon.com/blogs/compute/building-high-throughp…
    https://www.youtube.com/watch?v=v1DbcJD4Ry0
    broadinstitute.github.io/picard/explain-flags.html
    cole-trapnell-lab.github.io/cufflinks/manual/
    https://daehwankimlab.github.io/hisat2/
    subread.sourceforge.net/
    bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/…
    https://www.ncbi.nlm.nih.gov/genbank/
    https://pachterlab.github.io/kallisto/about
    https://www.ncbi.nlm.nih.gov/books/NBK47528/
    https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/
    rseqc.sourceforge.net/
    genome.ucsc.edu/FAQ/FAQformat.html
    bedtools.readthedocs.org/en/latest/
    samtools.github.io/hts-specs/SAMv1.pdf
    www.usadellab.org/cms/?page=trimmomatic
    tophat.cbcb.umd.edu/
    ryanstutorials.net/linuxtutorial/
    seqanswers.com/
    genome.ucsc.edu/ENCODE/downloads.html
    www.10xgenomics.com/10x-genomics/single-cell
    https://en.wikipedia.org/wiki/DNA_sequencing#High-throughpu…
    bowtie-bio.sourceforge.net/bowtie2/manual.shtml
    https://software.broadinstitute.org/gatk/blog?id=8180
    www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/v…
    ccb.jhu.edu/software/tophat/igenomes.shtml
    broadinstitute.github.io/picard/
    https://htseq.readthedocs.io/en/master/
    pachterlab.github.io/sleuth/about
    https://software.broadinstitute.org/gatk/documentation/
    www.broadinstitute.org/scientific-community/science/platfor…
Core NGS Tools (3)     Page: Analysis using BEDTools
    Page: Core NGS Resources
    Page: Linux fundamentals
Bioinformatics Team (BioITeam) at the University of Texas (3)     Page: Introduction to RNA Seq Course
    Page: Genome Variant Analysis Course 2017
    Page: Byte Club