> For the complete documentation index, see [llms.txt](https://book.ncrnalab.org/teaching/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://book.ncrnalab.org/teaching/appendix/appendix-v.-software-and-tools.md). # Appendix V. Software and Tools ## 0) Process files in different format ### 0.1) sequence * [seqtk](https://github.com/lh3/seqtk) * [bbmap](https://sourceforge.net/projects/bbmap/) ### 0.2) alignment * [gffread](https://github.com/gpertea/gffread) * [samtools](http://www.htslib.org/) * [bamtools](https://github.com/pezmaster31/bamtools) ### 0.3) interval * [bedtools](https://bedtools.readthedocs.io/en/latest/) * [bedtk](https://github.com/lh3/bedtk) ## 1) Homolog analysis ### 1.1) Sequence based search * [blast](https://blast.ncbi.nlm.nih.gov/Blast.cgi): 方便的网页工具 * [blat](https://genome.ucsc.edu/cgi-bin/hgBlat): a blast like tool * [mmseqs](https://github.com/soedinglab/MMseqs2): 比blast更现代的同源搜索工具，推荐本地进行大量计算时使用 * [diamond](https://github.com/bbuchfink/diamond): 蛋白的同源搜索工具 ### 1.2) Profile based search * [hmmer](http://hmmer.org/): profile hmm based search for protein and nucleotide sequence * [infernal](http://eddylab.org/infernal/): profile SCFG based search for structured noncoding RNA * [hh-suite](https://github.com/soedinglab/hh-suite): profile hmm to profile hmm alignment ### 1.3) Multiple sequence alignment * [MAFFT](https://mafft.cbrc.jp/alignment/software/) * [clustal](http://www.clustal.org/) * [T-Coffee](https://tcoffee.crg.eu/) ## 2) Genome Browsers * [UCSD Genome Browser](https://genome.ucsc.edu/) ([@youtube](https://youtu.be/eTgEtfI65hA) [@bilibili](https://player.bilibili.com/player.html?aid=30448417\&cid=53132461\&page=1)) * [IGV](http://software.broadinstitute.org/software/igv/) ([@youtube](https://youtu.be/6_1ZcVw7ptU) [@bilibili](https://player.bilibili.com/player.html?aid=30448472\&cid=53133093\&page=1)) > see more in [our Tutorial](/teaching/part-iii.-ngs-data-analyses/1.mapping/1.1-genome-browser.md) ## 3) DNA-seq ### (3.1) Mapping and QC * **Remove adaptor** * [cutadapt](https://cutadapt.readthedocs.io/en/stable/) * [TrimGalore](https://github.com/FelixKrueger/TrimGalore): 对cutadapt进行封装，自动识别常见adaptor * [Trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic) * [fastp](https://github.com/OpenGene/fastp) * **Mapping** * [bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) * [bowtie](https://bowtie-bio.sourceforge.net/manual.shtml) * [bwa](https://bio-bwa.sourceforge.net/) * **QC** * [fastqc](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) ### (3.2) Variant Calling * **Mutation discovery** * [GATK](https://gatk.broadinstitute.org/hc/en-us) * [Varscan](http://dkoboldt.github.io/varscan/) * **Mutation annotation** * [ANNOVAR](http://annovar.openbioinformatics.org/en/latest/user-guide/download/) ### (3.3) Assembly **denovo assembly software** * [SPAdes](https://github.com/ablab/spades) * the sub-utility metaSPAdes is designed for metagenome assembly * [megahit](https://github.com/voutcn/megahit): designed for metagenome assembly ### (3.4) CNV * **Whole genome Seq** * [Control-FREEC](http://boevalab.inf.ethz.ch/FREEC/) * **Whole exome Seq** * [CONTRA](http://contra-cnv.sourceforge.net/) * [ExomeCNV](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179661/) ### (3.5) SV (structural variation) * **structural variation** * [lumpy](https://github.com/arq5x/lumpy-sv) * [Breakdancer](http://breakdancer.sourceforge.net/) ## 4) RNA-seq ### (4.1) RNA-seq * **Mapping** * [STAR](https://github.com/alexdobin/STAR) * The sub-utility STARsolo is designed for mapping of single cell RNA-seq data * [hisat2](http://daehwankimlab.github.io/hisat2/) * **Expression Quantification** * [featureCounts](http://subread.sourceforge.net/) * [htseq-count](https://htseq.readthedocs.io/en/master/) * [salmon](https://combine-lab.github.io/salmon/) * [kallisto](https://pachterlab.github.io/kallisto/) * **Differential Analysis** * [deseq2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html) * [edgeR](https://bioconductor.org/packages/release/bioc/html/edgeR.html) * [limma](https://bioconductor.org/packages/release/bioc/html/limma.html) * **Alternative Splicing Analysis**: * [rMATS](http://rnaseq-mats.sourceforge.net/) * [MAJIQ](https://majiq.biociphers.org/) * [SUPPA](https://github.com/comprna/SUPPA) * [DEXSeq](https://bioconductor.org/packages/release/bioc/html/DEXSeq.html) * **RNA Editing** * [RNAEditor](http://rnaeditor.uni-frankfurt.de/) * [REDItools](http://code.google.com/p/reditools/) ### (4.2) Single Cell RNA-seq (scRNA-seq) * [awesome-single-cell](https://github.com/seandavi/awesome-single-cell): a collection of single cell analysis tools * [seurat](https://satijalab.org/seurat/): a widely used R package * [scanpy](https://scanpy.readthedocs.io/en/stable/): a widely used python package * [monocle](http://cole-trapnell-lab.github.io/monocle-release/): Trajectory analysis * [cellphonedb](https://www.cellphonedb.org/): Cell-cell interaction analysis * [scenic](https://scenic.aertslab.org/): Transcriptional regulatory network * Tutorials * * > [Nature Biotechnology 2020 38(3):254-257](https://www.nature.com/articles/s41587-020-0449-8) | Software name | Developer | Price structure | Platform-specific | Relevant stages of experiment | | -------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------- | --------------- | --------------------------- | ------------------------------------------------------------------------------------------------------------------------------------ | | [Cell Ranger](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-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](https://support.10xgenomics.com/single-cell-gene-expression/software/visualization/latest/what-is-loupe-cell-browser) | 10X Genomics | Free download | 10X Chromium | Visualization and analysis | | [Partek Flow](https://www.partek.com/application-page/single-cell-gene-expression/) | Partek | License | No | Complete data analysis and visualization pipeline for scRNA-seq data | | [Qlucore Omics Explorer](https://www.qlucore.com/single-cell-rnaseq) | Qlucore | License | No | scRNA-seq data filtering, dimensionality reduction and clustering, visualization | | [mappa Analysis Pipeline](https://www.takarabio.com/products/automation-systems/icell8-system-and-software/bioinformatics-tools/mappa-analysis-pipeline) | Takara Bio | Free download | Takara ICell8 | Raw read alignment and matrix generation for scRNA-seq | | [hanta R kit](https://www.takarabio.com/products/automation-systems/icell8-system-and-software/bioinformatics-tools/hanta-r-kit) | Takara Bio | Free download | Takara ICell8 | Clustering and analysis of mappa data | | [Singular Analysis Toolset](https://www.fluidigm.com/software) | Fluidigm | Free download | Fluidigm C1 or Biomark | Analysis and visualization of differential gene expression data for scRNA-seq | | [SeqGeq](https://www.flowjo.com/solutions/seqgeq) | FlowJo/BD Biosciences | License | No | Data normalization and QC, dimensionality reduction and clustering, analysis and visualization | | [Seven Bridges](https://www.sevenbridges.com/bdgenomics/) | Seven Bridges/BD Biosciences | License | BD Rhapsody and Precise | Cloud-based raw read alignment, QC and matrix generation | | [Tapestri Pipeline/Insights](https://missionbio.com/panels/software/) | Mission Bio | Free download | Mission Bio Tapestri | Analysis of single-cell genomics data | | [BaseSpace SureCell](https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub.html) | Illumina | License | Illumina SureCell libraries | Raw read alignment and matrix generation | | [OmicSoft Array Studio](https://omicsoftdocs.github.io/ArraySuiteDoc/tutorials/scRNAseq/Introduction/) | Qiagen | License | No | Raw read alignment, QC and matrix generation, dimensionality reduction and clustering | ### 4.3 Assembly * [Trinity](https://github.com/trinityrnaseq/trinityrnaseq/wiki): 利用RNA-seq数据进行转录本组装 ## 5) Interactome ### **(5.1) ChIP-seq** * [MACS](https://github.com/macs3-project/MACS): peak calling * [homer](http://homer.ucsd.edu/homer/): peak calling, motif finding, etc * [ChIPseeker](https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html): visualization and annotation ### **(5.2) CLIP-seq** * [CTK](https://zhanglab.c2b2.columbia.edu/index.php/CTK_Documentation) * [Piranha](http://smithlabresearch.org/software/piranha/) * [PARalyzer](https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/) * [clipper](https://github.com/YeoLab/clipper) ### **(5.3) Motif analysis** **sequence** 1. MEME motif based sequence analysis tools 2. HOMER Software for motif discovery and next-gen sequencing analysis **structure** 1. RNApromo Computational prediction of RNA structural motifs involved in post transcriptional regulatory processes 2. GraphProt modeling binding preferences of RNA-binding proteins ## 6) Epigenetic Data ### **(6.1) ChIP-seq** * **Bisulfate sequencing**: * Review: [Katarzyna Wreczycka, et al. Strategies for analyzing bisulfite sequencing data. Journal of Biotechnology. 2017.](https://www.sciencedirect.com/science/article/pii/S0168165617315936) * Mapping: * [Bismark](http://www.bioinformatics.babraham.ac.uk/projects/bismark/) * [BSMAP](https://github.com/zyndagj/BSMAPz) * Differential Methylation Regions (DMRs) detection * [methylkit](https://bioconductor.org/packages/release/bioc/html/methylKit.html) * [ComMet](https://github.com/yutaka-saito/ComMet) * Segmentation of the methylome, Classification of Fully Methylated Regions (FMRs), Unmethylated Regions (UMRs) and Low-Methylated Regions (LMRs) * [MethylSeekR](http://www.bioconductor.org/packages/release/bioc/html/MethylSeekR.html) * Annotation of DMRs * [genomation](https://bioconductor.org/packages/release/bioc/html/genomation.html) * [ChIPpeakAnno](https://www.bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html) * Web-based service * [WBSA](http://wbsa.big.ac.cn/) * **IP data**: * Overview to CHIP-Seq: * peak calling: [MACS2](https://github.com/taoliu/MACS/wiki/Advanced:-Call-peaks-using-MACS2-subcommands) * Peak annotation and visualization * [HOMER annotatePeak](http://homer.ucsd.edu/homer/ngs/annotation.html) * [ChIPseeker](http://bioconductor.org/packages/release/bioc/html/ChIPseeker.html) * Gene set enrichment analysis for ChIP-seq peaks * [GREAT](http://bejerano.stanford.edu/great/public/html/) ### **(6.2) DNAase-seq** * review : [Yongjing Liu, et al. Brief in Bioinformatics, 2019.](https://academic.oup.com/bib/article-abstract/20/5/1865/5053117?redirectedFrom=fulltext) * Peak calling: [F-Seq](http://fureylab.web.unc.edu/software/fseq/) * Peak annotation: [ChIPpeakAnno](https://www.bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html) * Motif analysis: [MEME-ChIP](http://meme-suite.org/doc/meme-chip.html?man_type=web) ### **(6.3) ATAC-seq** * Pipeline recommended by [Harward informatics](https://github.com/harvardinformatics/ATAC-seq) ### (7) Microbe data analysis * [kraken2](https://ccb.jhu.edu/software/kraken2/): k-mer based fast metagenome reads classification * [metaphlan](https://huttenhower.sph.harvard.edu/metaphlan/): marker gene based microbe taxonomy abundance estimation * [motu](https://motu-tool.org/): marker gene based microbe taxonomy abundance estimation * [maxbin](https://sourceforge.net/projects/maxbin/): binning contigs into metagenome-assembled genomes (MAGs) * [mash](https://mash.readthedocs.io/en/latest/distances.html): rapid estimation of distance between genome * [drep](https://drep.readthedocs.io/en/latest/): pick representative genome from sample-wise assembly * [prodigal](https://github.com/hyattpd/Prodigal): prokaryote gene prediction * [prokka](https://github.com/tseemann/prokka): pipeline for prokaryote genome annotation * [qiime2](https://qiime2.org/): 16S amplicon sequencing data analysis ## More: Shared tools and scripts * Scripts: [Lu Lab](https://github.com/lulab/shared_scripts) | [Zhi J. Lu](https://github.com/urluzhi/scripts) * Plots: [Lu Lab](/teaching/part-i.-programming-skills/2.r/2.2.plots-with-r.md) | [Zhi J. Lu](https://github.com/urluzhi/scripts/tree/master/Rscript/R_plot) ## 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](https://www.nature.com/articles/nbt.2721)