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Core NGS Tools Home
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Core NGS Resources
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Title:
Core NGS Resources
Author:
Anna M Battenhouse
May 11, 2014
Last Changed by:
Anna M Battenhouse
Jun 01, 2023
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https://wikis.utexas.edu/x/wrb5Aw
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Jun 01, 2023 22:21
Anna M Battenhouse
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Jun 11, 2022 17:30
Anna M Battenhouse
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Jun 08, 2021 03:32
Anna M Battenhouse
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Jun 08, 2021 03:24
Anna M Battenhouse
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Outgoing Links
External Links (92)
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://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/
https://wikis.utexas.edu/pages/viewpage.action?pageId=28165…
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/
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
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://www.gsea-msigdb.org
www.10xgenomics.com/
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
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…
Bioinformatics Team (BioITeam) at the University of Texas (3)
Page:
Introduction to RNA Seq Course
Page:
Genome Variant Analysis Course 2017
Page:
Byte Club
Core NGS Tools (3)
Page:
Analysis using BEDTools
Page:
Core NGS Resources
Page:
Linux fundamentals
Overview
Content Tools
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