11. 3rd Party Tools¶
11-1.Version 2.2.0¶
Octopus-toolkit utilizes the following 3rd party tools during the process.
| 3rd party tool | Version | Function |
|---|---|---|
Aspera |
v3.7.2.141527 | Download SRA files from NCBI |
SRAToolkit |
v2.9.2 | Convert SRA files to Fastq files |
FastQC |
v0.11.5 | Quality check for raw data |
Trimmomatic |
v0.36 | Trimming for adapter sequence and portions of low-quality reads |
Hisat2 |
v2.1.0 | Indexing and Mapping to reference genome |
STAR |
v2.5.1 | Indexing and Mapping to reference genome for RNA-Seq |
Homer |
v4.10.1 | Create bigWig for visualization and Detect enriched regions by mapped reads |
Bwtool, libbeato |
v1.0 | Calculate normalized values from bigWig files |
R |
v3.1 | Draw the heatmap and line plot |
IGV |
v2.7.2 | Explore the genome with processed data (bigWig files) |
Samtools |
v1.5 | Sorting and Indexing the mapped reads |