Appendix V. Software and Tools
- Remove adaptor
- QC
denovo assembly software
- Whole genome Seq
- structural variation
- Expression Quantification
- Tutorials
- https://bioconductor.org/books/release/OSCA/
- https://github.com/theislab/single-cell-tutorial
Software name | Developer | Price structure | Platform-specific | Relevant stages of experiment |
---|---|---|---|---|
10X Genomics | Free download | 10X Chromium | Raw read alignment, QC and matrix generation for scRNA-seq and ATAC-seq; data normalization; dimensionality reduction and clustering | |
10X Genomics | Free download | 10X Chromium | Visualization and analysis | |
Partek | License | No | Complete data analysis and visualization pipeline for scRNA-seq data | |
Qlucore | License | No | scRNA-seq data filtering, dimensionality reduction and clustering, visualization | |
Takara Bio | Free download | Takara ICell8 | Raw read alignment and matrix generation for scRNA-seq | |
Takara Bio | Free download | Takara ICell8 | Clustering and analysis of mappa data | |
Fluidigm | Free download | Fluidigm C1 or Biomark | Analysis and visualization of differential gene expression data for scRNA-seq | |
FlowJo/BD Biosciences | License | No | Data normalization and QC, dimensionality reduction and clustering, analysis and visualization | |
Seven Bridges/BD Biosciences | License | BD Rhapsody and Precise | Cloud-based raw read alignment, QC and matrix generation | |
Mission Bio | Free download | Mission Bio Tapestri | Analysis of single-cell genomics data | |
Illumina | License | Illumina SureCell libraries | Raw read alignment and matrix generation | |
Qiagen | License | No | Raw read alignment, QC and matrix generation, dimensionality reduction and clustering |
sequence
- 1.
- 2.HOMER Software for motif discovery and next-gen sequencing analysis http://homer.ucsd.edu/homer/motif/
structure
- 1.RNApromo Computational prediction of RNA structural motifs involved in post transcriptional regulatory processes https://genie.weizmann.ac.il/pubs/rnamotifs08/
- 2.GraphProt modeling binding preferences of RNA-binding proteins http://www.bioinf.uni-freiburg.de/Software/GraphProt/
- Bisulfate sequencing:
- Segmentation of the methylome, Classification of Fully Methylated Regions (FMRs), Unmethylated Regions (UMRs) and Low-Methylated Regions (LMRs)
- Annotation of DMRs
- Web-based service
- IP data:
- Peak annotation and visualization
- Gene set enrichment analysis for ChIP-seq peaks
Software | Purpose | Creators | Key capabilities | Year released | Citationsa |
---|---|---|---|---|---|
BLAST | Sequence alignment | Stephen Altschul, Warren Gish, Gene Myers, Webb Miller, David Lipman | First program to provide statistics for sequence alignment, combination of sensitivity and speed | 1990 | 35,617 |
R | Statistical analyses | Robert Gentleman, Ross Ihaka | Interactive statistical analysis, extendable by packages | 1996 | N/A |
ImageJ | Image analysis | Wayne Rasband | Flexibility and extensibility | 1997 | N/A |
Cytoscape | Network visualization and analysis | Trey Ideker et al. | Extendable by plugins | 2003 | 2,374 |
Bioconductor | Analysis of genomic data | Robert Gentleman et al. | Built on R, provides tools to enhance reproducibility of research | 2004 | 3,517 |
Galaxy | Web-based analysis platform | Anton Nekrutenko, James Taylor | Provides easy access to high-performance computing | 2005 | 309b |
MAQ | Short-read mapping | Heng Li, Richard Durbin | Integrated read mapping and SNP calling, introduced mapping quality scores | 2008 | 1,027 |
Bowtie | Short-read mapping | Ben Langmead, Cole Trapnell, Mihai Pop, Steven Salzberg | Fast alignment allowing gaps and mismatches based on Burrows-Wheeler Transform | 2009 | 1,871 |
Tophat | RNA-seq read mapping | Cole Trapnell, Lior Pachter, Steven Salzberg | Discovery of novel splice sites | 2009 | 817 |
BWA | Short-read mapping | Heng Li, Richard Durbin | Fast alignment allowing gaps and mismatches based on Burrows-Wheeler Transform | 2009 | 1,556 |
Circos | Data visualization | Martin Krzywinski et al. | Compact representation of similarities and differences arising from comparison between genomes | 2009 | 431 |
SAMtools | Short-read data format and utilities | Heng Li, Richard Durbin | Storage of large nucleotide sequence alignments | 2009 | 1,551 |
Cufflinks | RNA-seq analysis | Cole Trapnell, Steven Salzberg, Barbara Wold, Lior Pachter | Transcript assembly and quantification | 2010 | 710 |
IGV | Short-read data visualization | James Robinson et al. | Scalability, real-time data exploration | 2011 | 335 |
N/A, paper not available in Web of Science. | | | | | |