Appendix V. Software and Tools

1) Genome Browsers

see more in our Tutorial

2) DNA-seq

(2.1) Mapping and QC

(2.2) Mutation

(2.3) Assembly

  • denovo assembly software: Trinity

(2.4) CNV

(2.5) SV (structural variation)

3) RNA-seq

(3.1) RNA-seq

(3.2) Single Cell RNA-seq (scRNA-seq)

  • Selected Software providers for scRNA-seq analysis

Nature Biotechnology 2020 38(3):254-257

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.

4) Interactome

(4.1) ChIP-seq

(4.2) CLIP-seq

(4.3) Motif analysis

sequence

  1. MEME motif based sequence analysis tools http://meme-suite.org/

  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/

5) Epigenetic Data

(5.1) ChIP-seq

(5.2) DNAase-seq

(5.3) ATAC-seq

6) Chromatin and Hi-C

More: Lu Lab shared tools and scripts

More: Software for the ages

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