Table 4.
Widely used bioinformatics tools for the analysis of transcriptome data.
| Software | Description | Download URL | Reference |
|---|---|---|---|
| ABMapper | RNA-seq data alignment | http://hkbic.cuhk.edu.hk/software/abmapper | [91] |
| Bowtie | RNA-seq data alignment | http://bowtie-io.sourceforge.net/bowtie2/index.shtml | [92] |
| Cufflinks | Transcript assembly | http://cufflinks.cbcb.umd.edu/ | [93] |
| DEGseq | Differential gene expression detection | http://www.bioconductor.org/packages/2.11/bioc/html/DEGseq.html | [94] |
| Infernal | RNA-seq data alignment | http://infernal.janelia.org/ | [95] |
| Oases | De novo assembly | www.ebi.ac.uk/~zerbino/oases/ | [96] |
| Tophat | RNA-seq data alignment & Alternative splicing detection | http://tophat.cbcb.umd.edu/ | [97] |
| Trans-AByss | De novo assembly | http://www.bcgsc.ca/platform/bioinfo/software/ | [98] |
| Trinity | De novo assembly | http://trinityrnaseq.sourceforge.net/ | [99] |