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Bioinformatics Services
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CBRS Mini Symposium
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BCG Full Service Pipelines
zArchive
TACC stuff
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Old Home page
Old BCG Full Service Pipelines
Training
Software
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ABI's SOLiD de novo pipeline
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ABYSS
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Annovar
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BFAST
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Bioconductor
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BioMart Perl APIs
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Blast
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BLAST tools
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BOOST libraries
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Bowtie
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Breakdancer
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BWA
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BWA-SAMTOOLS workflow
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CASAVA
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Circos
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CGView
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Clustering programs - MCL and usearch, uclust
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Conversion of gene ID's from one form to another (i.e. NCBI to Ensembl & vice-versa)
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Conversion of mapreads output to GFF, SAM, or BAM format
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Convert ABI SOLiD data to fasta fastq
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Cufflinks
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Data compression programs
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Extracting barcode split data from SOLiD 5500 XSQ files
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FastQC
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Fastx Toolkit
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Galaxy Setup
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Geneid
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General parser scripts
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Generation of gene counts from results of mapping to genome
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Generation of wig files from mapreads output
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GeneWise
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Genome Analysis Tool Kit
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Getting an account on GSAF server-fourierseq
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Get Tm (melting temperature), length, and %GC from a bunch of sequences
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glimmer3
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GMAP and GSNAP
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Graphic programs
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GS Amplicon variant analyzer
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GS De novo assembler
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GS Reference mapper
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GS Run processor and run browser
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Hmmer
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IGV
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Make a quick venn diagram based on lists in 3 files
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mapreads
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MAQ
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MaqView
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Median polish to consolidate quantitations
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MegaMapper
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MeV
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MIRA
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Mosaik
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muscle
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Phred, Phrap, Consed, cross_match, daev
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Picard
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Plot a read length histogram based on sequences in a fasta file
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Python Library
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Quick tips on GO analysis
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R and R packages
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Reverse complement for fasta files
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RNA-seq workflow
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SAMTOOLS
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Sff file manipulation tools
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SHRiMP
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Small rna analysis
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Small-rna data analysis
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Small RNA Pipeline
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SOAP
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SOAPtrans
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Tips for working with TACC resources
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Tophat- Cufflinks
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Tophat-Cufflinks-Cuffdiff, allowing for novel transcripts
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Tophat-Cufflinks-Cuffdiff, ignoring novel transcripts
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Tricks to preprocess SOLiD and 454 data
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Trinity
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Variant calling
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Velvet
ZOHO Information
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Removing duplicates from alignment output
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SAMStat
TACC Lonestar workflow scripts
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Get FASTQ Format
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launcher_creator.py
Wrappers For TACC