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