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| Software | Description | Path | in rna_sequencing_client.pp |
|---|---|---|---|
| augustus | program to find genes and their structures in one or more genomes | y | |
| busco | y | ||
| cellranger | y | ||
| cufflinks | y | ||
| express | Expression quantification | /usr/bin/express | y |
| fastqc | y | ||
| featurecounts | Counting | /usr/bin/featureCounts | y |
| htseq | Counting | /stor/system/opt/HTSeq-0.6.1p1 | y |
| kallisto | Expression quantification | /usr/bin/kallisto | y |
| STAR | Alignment | /usr/bin/STAR /usr/bin/STARlong | y |
| tophat | y | ||
| MultiQC | Report Generation | /usr/bin/multiqc | y |
| RNA-SeQC | QC of RNA-seq alignments. To run this Java program: java -jar /stor/system/opt/rnaseqc/RNA-SeQC_v1.1.8.jar <other options> | /stor/system/opt/rnaseqc | y |
| salmon | y | ||
| 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 reference genome | /stor/system/opt/hisat2-2.0.5/ | |
| gossamer | bioinformatics suite including goss, gossple, xenome, and electus | /usr/local/bin/goss /usr/local/bin/gossple /usr/local/bin/xenome /usr/local/bin/electus | y |
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