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Software | Description | Path | in rna_sequencing_client.pp |
---|---|---|---|
augustus | 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 |
Specialized NGS Tools
(specialized_sequencing_client.pp)
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