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Title: Software  
Author: Scott Patrick Hunicke-Smith Apr 28, 2011
Last Changed by: Scott Patrick Hunicke-Smith Jul 25, 2013
Tiny Link: (useful for email) https://wikis.utexas.edu/x/rxtQAQ
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Genomic Sequencing and Analysis Facility User Support Wiki (1)
    Page: About Us
Hierarchy
Parent Page
    Page: zArchive
Children (85)
    Page: ABI's SOLiD de novo pipeline
    Page: ABYSS
    Page: Annovar
    Page: BFAST
    Page: Bioconductor
    Page: BioMart Perl APIs
    Page: Blast
    Page: BLAST tools
    Page: BOOST libraries
    Page: Bowtie
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Outgoing Links
External Links (3)
    www.affymetrix.com/partners_programs/programs/developer/too…
    https://wikis.utexas.edu/display/bioiteam/TACC+Genomics+Mod…
    https://wikis.utexas.edu/display/bioiteam/SOAPtrans
Bioinformatics Team (BioITeam) at the University of Texas (77)     Page: Fastx Toolkit
    Page: MaqView
    Page: Get Tm (melting temperature), length, and %GC from a bunch of sequences
    Page: GS De novo assembler
    Page: GS Amplicon variant analyzer
    Page: Python Library
    Page: BFAST
    Page: Breakdancer
    Page: Tips for working with TACC resources
    Page: GeneWise
    Page: glimmer3
    Page: Clustering programs - MCL and usearch, uclust
    Page: GS Reference mapper
    Page: Generation of gene counts from results of mapping to genome
    Page: Plot a read length histogram based on sequences in a fasta file
    Page: SOAP
    Page: GMAP and GSNAP
    Page: Small RNA Pipeline
    Page: Small rna analysis
    Page: IGV
    Page: Bowtie
    Page: GS Run processor and run browser
    Page: Trinity
    Page: SAMTOOLS
    Page: Annovar
    Page: Phred, Phrap, Consed, cross_match, daev
    Page: SAMStat
    Page: Picard
    Page: Variant calling
    Page: Convert ABI SOLiD data to fasta fastq
    Page: Genome Analysis Tool Kit
    Page: BWA
    Page: Conversion of mapreads output to GFF, SAM, or BAM format
    Page: Velvet
    Page: FastQC
    Page: Data compression programs
    Page: muscle
    Page: ABI's SOLiD de novo pipeline
    Page: Tophat-Cufflinks-Cuffdiff, allowing for novel transcripts
    Page: Extracting barcode split data from SOLiD 5500 XSQ files
    Page: Make a quick venn diagram based on lists in 3 files
    Page: Tophat- Cufflinks
    Page: Sff file manipulation tools
    Page: MeV
    Page: Tricks to preprocess SOLiD and 454 data
    Page: ZOHO Information
    Page: ssh - generating keys
    Page: Conversion of gene ID's from one form to another (i.e. NCBI to Ensembl & vice-versa)
    Page: BOOST libraries
    Page: MIRA
    Page: R and R packages
    Page: Circos
    Page: Bioconductor
    Page: Blast
    Page: Getting started with Unix and Perl
    Page: Geneid
    Page: ABYSS
    Page: Getting an account on GSAF server-fourierseq
    Page: RNA-seq workflow
    Page: Quick tips on GO analysis
    Page: BLAST tools
    Page: mapreads
    Page: Median polish to consolidate quantitations
    Page: BioMart Perl APIs
    Page: Mosaik
    Page: MAQ
    Page: Hmmer
    Page: Get FASTQ Format
    Page: Removing duplicates from alignment output
    Page: Reverse complement for fasta files
    Page: Generation of wig files from mapreads output
    Page: Tophat-Cufflinks-Cuffdiff, ignoring novel transcripts
    Page: BWA-SAMTOOLS workflow
    Page: SHRiMP
    Page: TACC Lonestar workflow scripts
    Page: General parser scripts
    Page: Small-rna data analysis