Table 2.
The list of AS analysis tools chosen for benchmark
| Name (version) | Dependencies | Reference | Genome Annotation* |
|---|---|---|---|
| A. Splice-aware mapping tools | |||
| BBMap (38.94) | Java 7+ | (24) | - |
| ContextMap2 (2.7.9) | Java, BWA, bowtie 1, bowtie2 | (26) | + |
| In the current study used with bowtie 2 (25) | |||
| CRAC (2.5.2) | Perl, htslib | (27) | - |
| DART (1.4.6) | GCC, GNU make, libboost-all-dev, | (28) | - |
| libbz2-dev, and liblzma-dev | |||
| GSNAP (2020-03-12) | GCC,GNU make, Perl | (29) | + |
| HISAT2 (2.2.1) | GCC, GNU make, MSYS, zlib | (30) | + |
| MapSplice2 (2.2.1) | GCC 4.3.3+, GNU make, python 2+ | (31) | + |
| minimap2 (2.17) | None (precompiled binaries) or | (32) | - |
| GCC, GNU make, zlib | |||
| segemehl (0.3.4) | GCC, GNU make, htslib | (33) | - |
| STAR (2.7.5) | GCC, GNU make | (34) | + |
| Subjunc (2.0.0) | None (precompiled binaries) or | (35) | + |
| GCC, GNU make | |||
| B. Alternative splicing event detection tools | |||
| Name (version) | Dependencies | Reference | Supported events |
| ASGAL (1.1.6) | python3.6+, biopython, pysam, gffutils, | (36) | ES, IR, A5, A3 |
| pandas, cmake, samtools, zlib | |||
| ASpli (1.12.0) | R, BiocManager | (37) | ES, IR, A5 A3 |
| EventPointer (2.4.0) | R, BiocManager | (38) | ES, IR, A5, A3, MEE, MES |
| IRFinder (1.3.1) | GLIBC 2.14+, GCC 4.9.0+, Perl 5+, | ||
| STAR 2.4.0+, samtools 1.4+, bedtools 2.4+ | (39) | IR | |
| MAJIQ (2.3) | htsilb, python3, python packages | (23) | ES, IR, A5, A3 |
| SGSeq (1.24.0) | R, BiocManager | (40) | ES, IR, A5, A3SS, AFE, |
| ALE, AF, AL, | |||
| MES (with two skipped exons) | |||
| splAdder (2.4.3) | python3, python packages | (41) | ES, IR, A5, A3, MEE, MES |
| Whippet (0.11.1) | julia | (42) | New junctions could be |
| added from alignment as an option | |||
| ES, A3SS, A5SS, IR, AFE, ALE, | |||
| tandem transcription start, tandem | |||
| alternative polyadenylation, circular | |||
| back splicing |
* ‘-’: does not use; ‘+’ - can use as an option
ES, exon skipping; IR, intron retention; A3, alternative 3′-splice site, A5, alternative 5′-splice site, MES, multiple exon skipping, MEE, mutually exclusive exons, AFE, alternative first exon, ALE, alternative last exon.