Appendix V. Software and Tools
0) Process files in different format
0.1) sequence
0.2) alignment
0.3) interval
1) Homolog analysis
1.1) Sequence based search
1.2) Profile based search
hmmer: profile hmm based search for protein and nucleotide sequence
infernal: profile SCFG based search for structured noncoding RNA
hh-suite: profile hmm to profile hmm alignment
1.3) Multiple sequence alignment
2) Genome Browsers
see more in our Tutorial
3) DNA-seq
(3.1) Mapping and QC
Remove adaptor
TrimGalore: 对cutadapt进行封装，自动识别常见adaptor
QC
(3.2) Variant Calling
Mutation annotation
(3.3) Assembly
denovo assembly software
the sub-utility metaSPAdes is designed for metagenome assembly
megahit: designed for metagenome assembly
(3.4) CNV
Whole genome Seq
(3.5) SV (structural variation)
structural variation
4) RNA-seq
(4.1) RNA-seq
Expression Quantification
(4.2) Single Cell RNA-seq (scRNA-seq)
awesome-single-cell: a collection of single cell analysis tools
seurat: a widely used R package
scanpy: a widely used python package
monocle: Trajectory analysis
cellphonedb: Cell-cell interaction analysis
scenic: Transcriptional regulatory network
Tutorials
https://bioconductor.org/books/release/OSCA/
https://github.com/theislab/single-cell-tutorial
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
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
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
4.3 Assembly
Trinity: 利用RNA-seq数据进行转录本组装
5) Interactome
(5.1) ChIP-seq
MACS: peak calling
homer: peak calling, motif finding, etc
ChIPseeker: visualization and annotation
(5.2) CLIP-seq
(5.3) Motif analysis
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/
6) Epigenetic Data
(6.1) ChIP-seq
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:
Overview to CHIP-Seq: https://github.com/crazyhottommy/ChIP-seq-analysis
peak calling: MACS2
Peak annotation and visualization
Gene set enrichment analysis for ChIP-seq peaks
(6.2) DNAase-seq
Peak calling: F-Seq
Peak annotation: ChIPpeakAnno
Motif analysis: MEME-ChIP
(6.3) ATAC-seq
Pipeline recommended by Harward informatics
(7) Microbe data analysis
kraken2: k-mer based fast metagenome reads classification
metaphlan: marker gene based microbe taxonomy abundance estimation
motu: marker gene based microbe taxonomy abundance estimation
maxbin: binning contigs into metagenome-assembled genomes (MAGs)
mash: rapid estimation of distance between genome
drep: pick representative genome from sample-wise assembly
prodigal: prokaryote gene prediction
prokka: pipeline for prokaryote genome annotation
qiime2: 16S amplicon sequencing data analysis
More: Shared tools and scripts
More: Software for the ages
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
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