...
| Software | Description | Path |
|---|---|---|
| express | Expression quantification | /usr/bin/express |
| featurecounts | Counting | /usr/bin/featureCounts |
| htseq | Counting | /stor/system/opt/HTSeq-0.6.1p1 |
| kallisto | Expression quantification | /usr/bin/kallisto |
| STAR | Alignment | /usr/bin/STAR /usr/bin/STARlong |
| MultiQC | Report Generation | /usr/bin/multiqc |
| hisat | spliced alignment for mapping RNA-seq reads | /stor/system/opt/hisat-0.1.6-beta |
| hisat2 | align NGS reads (both DNA and RNA) against a genome population | /stor/system/opt/hisat2-2.0.5/ |
Specialized NGS Tools
| Software | Description | Path |
|---|---|---|
| MultiQC | Report Generation | /usr/bin/multiqc |
| eisen cluster | hierachical & k-means clustering | /usr/bin/cluster-eisen |
| meme suite | motif analysis | /stor/system/opt/meme_4.11.2 |
| meme_chip | motif analysis suite for ChIP-seq | /stor/system/opt/software/meme-chip/4.11.2/ |
| art | next generation sequencing read simulator | /usr/bin/art_454 /usr/bin/art_illumina /usr/bin/art_SOLiD |
Variant Analysis Tools
NB: These tools are only available on select PODs. At this time of this writing, it included the GSAF and Iyer PODs.
...
| Software | Description | Location | Path |
|---|---|---|---|
| bam2fastq | Iyer POD | /stor/system/opt/bam2fastq-1.1.0/ | |
| docker | Marcotte POD | ||
| irodsfs | Not yet fully supported | gsafcbig01 | /mnt/corral |
| jupiterhub | Python Notebook Server | gsafcbig01 gsafcbig02 ccbbcomp02 | https://gsafcbig01.ccbb.utexas.edu/ |
| R Server | R Studio Web Interface | lambcomp01 iyercomp03 marccomp01 wcarcomp01 | https://lambcomp01.ccbb.utexas.edu/ |
| R caTools | Iyer POD | ||
| R snow | Iyer POD | ||
| R phantompeakqualtools | Iyer POD | ||
| R NCIS | Iyer POD |