see more in our Tutorial
- Remove adaptor: cutadapt, Trimmomatic
- Mapping: Bowtie2, STAR
- QC: fastqc
- denovo assembly software: Trinity
- Whole Genome Seq: Control-FREEC
- Whole exome Seq: CONTRA, ExomeCNV
- structural variation: Breakdancer
- Expression Matrix: featureCounts, HTseq
- Differential Expression: Deseq2, EdgeR
- Alternative Splicing: rMATS
- RNA Editing: RNAEditor, REDItools
- ...
- Selected Software providers for scRNA-seq analysis
| Software name | Developer | Price structure | Platform-specific | Relevant stages of experiment |
|---|---|---|---|---|
| Cell Ranger | 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 |
| Loupe Cell Browser | 10X Genomics | Free download | 10X Chromium | Visualization and analysis |
| Partek Flow | Partek | License | No | Complete data analysis and visualization pipeline for scRNA-seq data |
| Qlucore Omics Explorer | Qlucore | License | No | scRNA-seq data filtering, dimensionality reduction and clustering, visualization |
| mappa Analysis Pipeline | Takara Bio | Free download | Takara ICell8 | Raw read alignment and matrix generation for scRNA-seq |
| hanta R kit | Takara Bio | Free download | Takara ICell8 | Clustering and analysis of mappa data |
| Singular Analysis Toolset | Fluidigm | Free download | Fluidigm C1 or Biomark | Analysis and visualization of differential gene expression data for scRNA-seq |
| SeqGeq | FlowJo/BD Biosciences | License | No | Data normalization and QC, dimensionality reduction and clustering, analysis and visualization |
| Seven Bridges | Seven Bridges/BD Biosciences | License | BD Rhapsody and Precise | Cloud-based raw read alignment, QC and matrix generation |
| Tapestri Pipeline/Insights | Mission Bio | Free download | Mission Bio Tapestri | Analysis of single-cell genomics data |
| BaseSpace SureCell | Illumina | License | Illumina SureCell libraries | Raw read alignment and matrix generation |
| OmicSoft Array Studio | Qiagen | License | No | Raw read alignment, QC and matrix generation, dimensionality reduction and clustering |
QC, quality control; ATAC-seq, assay for transposase-accessible chromatin using sequencing.
sequence
- MEME motif based sequence analysis tools http://meme-suite.org/
- HOMER Software for motif discovery and next-gen sequencing analysis http://homer.ucsd.edu/homer/motif/
structure
- RNApromo Computational prediction of RNA structural motifs involved in post transcriptional regulatory processes https://genie.weizmann.ac.il/pubs/rnamotifs08/
- GraphProt modeling binding preferences of RNA-binding proteins http://www.bioinf.uni-freiburg.de/Software/GraphProt/
- Bi-sulfate data:
- Review: Katarzyna Wreczycka, et al. Strategies for analyzing bisulfite sequencing data. Journal of Biotechnology. 2017.
- Mapping: Bismark, BSMAP
- Differential Methylation Regions (DMRs) detection: methylkit, ComMet
- Segmentation of the methylome, Classification of Fully Methylated Regions (FMRs), Unmethylated Regions (UMRs) and Low-Methylated Regions (LMRs): MethylSeekR
- Annotation of DMRs: genomation, ChIPpeakAnno
- Web-based service: WBSA
- IP data:
- Overview to CHIP-Seq: https://github.com/crazyhottommy/ChIP-seq-analysis
- peak calling: MACS2
- Peak annotation: HOMER annotatePeak, ChIPseeker
- Gene set enrichment analysis for ChIP-seq peaks: GREAT
- review : Yongjing Liu, et al. Brief in Bioinformatics, 2019.
- peek calling: F-Seq
- peek annotation: ChIPpeakAnno
- Motif analysis: MEME-ChIP
- pipeline recommended by Harward informatics
- peek calling: MACS2
- peak annotation: ChIPseeker
- Motif discovery: HOMER
| 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. |
From: The anatomy of successful computational biology software