| Function |
Name |
Full Term |
Contributors |
Ref. |
| ChIP-Seq |
| Mapping |
MAQ |
Mapping and Assembly with Quality |
Durbin et al., The Wellcome Trust Sanger Institute, UK |
[53] |
| Bowtie/Bowtie2 |
--- |
Langmead et al., University of Maryland, USA |
[54, 55] |
| BWA |
Burrows-Wheeler Aligner |
Durbin et al., The Wellcome Trust Sanger Institute, UK |
[56, 57] |
|
Calling Peaks |
FindPeaks |
--- |
Fejes et al., BC Cancer Agency, Canada |
[69] |
| peakSeq |
--- |
Rozowsky et al., Yale University, USA |
[70] |
| cisGenome |
--- |
Wong et al., Stanford University, USA |
[71] |
| SiSSRs |
Site Identification from Short Sequence Reads |
Zhao et al., National Institutes of Health, USA |
[72] |
| QuEST |
Quantitative Enrichment of Sequence Tags |
Sidow et al., Stanford University, USA |
[16] |
| MACS |
Model-based Analysis of ChIP-Seq |
Liu et al., Harvard University, USA |
[73] |
| USeq |
--- |
Nix et al., University of Utah, USA |
[78] |
| RNA-Seq |
| Mapping |
TopHat |
--- |
Salzberg et al., The Johns Hopkins University, USA |
[62] |
| ERANGE |
Enhanced Read Analysis of Gene Expression |
Wold et al., California Institute of Technology, USA |
[63] |
| QPALMA |
Optimal Spliced Alignments of Short Sequence Reads |
Rätsch et al., Max Planck Society, Germany |
[64] |
| Subread |
--- |
Shi et al., The University of Melbourne, Australia |
[65] |
| STAR |
Spliced Transcripts Alignment to a Reference |
Dobin et al., Cold Spring Harbor Laboratory, USA |
[66] |
| HISAT |
Hierarchical Indexing for Spliced Alignment of Transcripts |
Salzberg et al., The Johns Hopkins University, USA |
[67] |
| RPKM/FPKM calculations |
IsoInfer |
Inference of isoforms |
Fenget al., Tongji University, China |
[79] |
| Scripture |
--- |
Guttman et al., Massachusetts Institute of Technology, USA |
[80] |
| SLIDE |
Sparse linear modeling of RNA-Seq data for isoform discovery and abundance estimation |
Huang et al., University of California, Berkeley, USA |
[81] |
| IsoLasso |
Isoforms of Least Absolute Shrinkage and Selection Operator |
Li et al.,University of California, Riverside, USA |
[82] |
| iReckon |
Isoform reconstruction and abundance estimation |
Brudno et al.,University of Toronto, Canada |
[83] |
| Traph |
Transcripts in gRAPHs |
Tomescu et al., University of Helsinki, Finland |
[84] |
| Cufflinks |
--- |
Pachter et al., University of California, Berkeley, USA |
[85] |
| MiTie |
Mixed Integer Transcript IdEntification |
Behr et al., Sloan-Kettering Institute, USA |
[86] |
| StringTie |
--- |
Salzberg et al., The Johns Hopkins University, USA |
[87] |
| MethylC-Seq |
| Mapping and determine of T/C ratio |
BSMap |
Bisulfite sequence MAPping |
Li et al., Baylor College of Medicine, USA |
[58] |
| Bismark |
--- |
Krueger et al., The Babraham Institute, UK |
[59] |
| BS-Seeker |
Precise mapping for bisulfite sequencing |
Pellegrini et al., University of California, Los Angeles, USA |
[60] |
| MethylCoder |
--- |
Pedersen et al., University of California, Berkeley, USA |
[61] |
