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Bioinformatics Team Home
zArchive
Software
Page Information
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
Export As:
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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
Show all...
Page:
Breakdancer
Page:
BWA
Page:
BWA-SAMTOOLS workflow
Page:
CASAVA
Page:
Circos
Page:
CGView
Page:
Clustering programs - MCL and usearch, uclust
Page:
Conversion of gene ID's from one form to another (i.e. NCBI to Ensembl & vice-versa)
Page:
Conversion of mapreads output to GFF, SAM, or BAM format
Page:
Convert ABI SOLiD data to fasta fastq
Page:
Cufflinks
Page:
Data compression programs
Page:
Extracting barcode split data from SOLiD 5500 XSQ files
Page:
FastQC
Page:
Fastx Toolkit
Page:
Galaxy Setup
Page:
Geneid
Page:
General parser scripts
Page:
Generation of gene counts from results of mapping to genome
Page:
Generation of wig files from mapreads output
Page:
GeneWise
Page:
Genome Analysis Tool Kit
Page:
Getting an account on GSAF server-fourierseq
Page:
Get Tm (melting temperature), length, and %GC from a bunch of sequences
Page:
glimmer3
Page:
GMAP and GSNAP
Page:
Graphic programs
Page:
GS Amplicon variant analyzer
Page:
GS De novo assembler
Page:
GS Reference mapper
Page:
GS Run processor and run browser
Page:
Hmmer
Page:
IGV
Page:
Make a quick venn diagram based on lists in 3 files
Page:
mapreads
Page:
MAQ
Page:
MaqView
Page:
Median polish to consolidate quantitations
Page:
MegaMapper
Page:
MeV
Page:
MIRA
Page:
Mosaik
Page:
muscle
Page:
Phred, Phrap, Consed, cross_match, daev
Page:
Picard
Page:
Plot a read length histogram based on sequences in a fasta file
Page:
Python Library
Page:
Quick tips on GO analysis
Page:
R and R packages
Page:
Reverse complement for fasta files
Page:
RNA-seq workflow
Page:
SAMTOOLS
Page:
Sff file manipulation tools
Page:
SHRiMP
Page:
Small rna analysis
Page:
Small-rna data analysis
Page:
Small RNA Pipeline
Page:
SOAP
Page:
SOAPtrans
Page:
Tips for working with TACC resources
Page:
Tophat- Cufflinks
Page:
Tophat-Cufflinks-Cuffdiff, allowing for novel transcripts
Page:
Tophat-Cufflinks-Cuffdiff, ignoring novel transcripts
Page:
Tricks to preprocess SOLiD and 454 data
Page:
Trinity
Page:
Variant calling
Page:
Velvet
Page:
ZOHO Information
Page:
Removing duplicates from alignment output
Page:
SAMStat
Page:
TACC Lonestar workflow scripts
Page:
Get FASTQ Format
Page:
launcher_creator.py
Page:
Wrappers For TACC
Page:
ssh - generating keys
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Recent Changes
Time
Editor
Jul 25, 2013 04:45
Scott Patrick Hunicke-Smith
View Changes
Migrated to Confluence 5.3
Jul 25, 2013 04:45
Scott Patrick Hunicke-Smith
View Changes
Mar 25, 2013 12:08
Dhivya Arasappan
View Changes
Migrated to Confluence 4.0
Mar 25, 2013 12:08
Dhivya Arasappan
View Changes
Dec 13, 2012 11:10
Benjamin M Goetz
View Page History
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
Overview
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