Bioinformatics for CRISPR Biology
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Welcome to a comparison between software for analysing CRISPR-Cas loci in microbial genomes
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The systems consist of a 1) CRISPR ncRNA arrays, 2) Cas proteins, 3) possibly a tracrRNA and 4) target. Other nucleic acids (e.g. bacteriophage viral genomes)
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Email suggestions to the Author, Chris Brown
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Main function
Methods used DNA, protein
Web toolIn other PipelineSource available from:Local install
Speed s/genome
RNA DirectionUser control (score 1-5)Graphic output
Detailed output (score 1-5)
Major AdvantageMajor limitationCommentsInput format
Output format
Total cites by 2019Link to google citationReference
Omicstools link
Other weblink
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1A Genome analysis (including draft genomes)
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CRISPRDetect (2016)Find CRISPR (Type)blastn, waterYesYes
https://github.com/davidchyou/CRISPRDetect_2.4
cli5
Yes (CRISPRDirection)
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Web based, link to CRISPRTarget (currently not implemented)
Type classification poor
Integrated with other tools
fa, gbk, gbff
CD format, tab
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https://scholar.google.com/scholar?cites=16988424485819597285&as_sdt=2005&sciodt=0,5&hl=en
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CRISPRFinder (2007) SupercededFind CRISPRblastnYesYesNANANo322Well known and cited
Does not predict direction
Integrated with other tools
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https://scholar.google.com/scholar?cites=9274675655186029064&as_sdt=2005&sciodt=0,5&hl=en
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CRT (2007)Find CRISPRexact k-merNoNCBI, JGIcliNo111Has been incorporated into pipelines
Does not predict direction
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Piler-CR (2007)Find CRISPRNoNCBI, JGIcliNo111Has been incorporated into pipelines
Does not predict direction
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Minced (2014) Find CRISPR
exact k-mer (as CRT)
Yes
Prokka, CRISPRDisco
No111Automatic with CDS annotation in prokka
Does not predict direction
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CRISPRCompar (2008)Find CRISPR, CasYesNoNo32Only program that compares arrays
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CRISPRone Find CRISPR, CasYesNoNANA2
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CRISPRCasFinder (2018)Find CRISPR, CasYesNoDocker
Yes (CRISPRDirection)
4Self target, PAM 71
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STSS (2018)Find CRISPR, Cas, Type, Detect Self matchblastnNoNo
Finds self targets
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CRISPRDisco (2018)Find CRISPR, CasblastnNoYeshttps://github.com/crisprlab/CRISPRdisco
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CRF (2017)Find CRISPR RNA
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CasLocusAnnoFind Cas
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CRISPRCasTyper (2020)Find CRISPR, Cas, TypeYesNo
https://github.com/Russel88/CRISPRCasTyper
Yes
https://crisprcastyper.crispr.dk/
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CRISPRIdentify (2020)Find CRISPR, Cas, Type(No)No
https://github.com/BackofenLab/CRISPRidentify
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1B Metagenome analysis (reads or contigs)
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Meta-CRTFind CRISPR in metagenomeNo
https://omictools.com/metacrt-tool
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Crass (2013)Find CRISPR in metagenomeNo
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metaCRISPR (2016)Find CRISPR in metagenomeNohttps://github.com/hangelwen/metaCRISPRcli, git
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CasCollect (2019) Cas in raw reads Nohttps://github.com/sandialabs/CasCollectcli, git
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CRISPRCasMeta (unpublished 2019)CRISPR-Cas in raw readsYes
https://crisprcas.i2bc.paris-saclay.fr/CrisprCasMeta/Index
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metaCRISPRDetect (Biswas, unpublished)
CRISPR-Cas in raw reads
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1C CRISPR type classification
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CRISPRMap (2013)Repeat ClassificationYesNo
Yes (CRISPRStrand)
23Only focussed repeat/type classification tool
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CRISPRMiner (2018)CRISPR arrays and Cas protein annotation, CRISPR-Cas system classification, self-targeting events detection, microbe–phage interaction inference, and anti-CRISPR annotationYes10
https://scholar.google.com/scholar?cites=6275573734033564042&as_sdt=2005&sciodt=0,5&hl=en
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2) Cas proteins
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Usually detected by automated annotation in pipelines - can use hmm (e.g from Makarova et al 2015 or Burstein et al 2015)
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CRISPRDisco, STSS, CasFinder, CasCollect, etc
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3) TracrRNA
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TracrRNAfinder (Chyou et al 2019)
Find CRISPR using CRISPRDetect, Cas9 using PSIBLAST and HMMsearch, and then find tracrRNAblastn, hmmerYesNogithubNA
Yes (algorithm run on both strands)
Only general-purpose tracrRNA predictor. CRISPR Array direction not required. Can predict tracrRNAs with no significant similarity between anti-repeat and repeat.
Lack of a good reliability score
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4) Spacer Target analysis
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CRISPRTarget (2013)Find spacer targetblastn, waterYesNoNoOnly focussed target toolSlow, only onlineScore +1/-1
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blastn -mode shortFind spacer targetblastnYesNoNCBIGeneric program, faster
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5) CRISPR Leader/Promoter analysis
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CRISPRLeader (2016)Promoter alignmentNoNo
http://www.bioinf.uni-freiburg.de/Software/CRISPRleader/
Only focussed leader tool
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6) AntiCRISPRs Acr/Aca
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AntiCRISPR database (2017)AcR database of known Acr
http://cefg.uestc.cn/anti-CRISPRdb/
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AcrCatalog AcR database of known and predicted
http://bcb.unl.edu/AcrDB/
https://msystems.asm.org/content/4/5/e00455-19.abstract
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acRanker (2020)AntiCRISPR discovery
http://acranker.pythonanywhere.com/
https://github.com/amina01/AcRanker
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acrfinder (2020)AntiCRISPR discovery
http://bcb.unl.edu/AcrFinder)
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PaCRISPRAntiCRISPR discovery
pacrispr.erc.monash.edu/.
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AcrDetectorAntiCRISPR discovery
https://www.biorxiv.org/content/10.1101/2020.05.23.112011v1.abstract
https://github.com/RiversDong/AcrDetector
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7) Focus on Visualisation
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CRISPRViz (2018)Predicts (crt) and Visualises multiple arraysNohttps://github.com/CRISPRlab/CRISPRviz
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CRISPRStudio (2018)Visualises array, CRISPRDetect input
https://usegalaxy.eu/
github
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CRISPRCasViewer (2018)Visualises array and Cas genes from CRISPRCasFinderYes
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7) Host detection via CRISPR
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CRISPRHost (2020)) Unpublishedblastn
Yes, galaxy 139.80.3.3:8080
https://github.com/davidchyou/CRISPRHost_data_analysis
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SpacePHARER (2020)https://github.com/soedinglab/MMseqs2
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CRISPRBlast (2016)Yes, JGI
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8) Other
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CRISPRDirection (2014)Predicts direction of arrayNoYesIncluded in CRISPRDetect
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CRISPRStrand (2014)Predicts direction of arrayNoYesIncluded in CRISPRMap
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CRISPRCasDBtaxo (unpublished)Yes
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CLdb (unpublished, 2014?)LotsNohttps://github.com/nick-youngblut/CLdbYes
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dnasko/CASC: CASC Ain't Simply CRT
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GitHub - TrinhLab/CASPERpam: Python code and source files used to identify and analyze PAM sequences for the complete NCBI spacerome
https://github.com/TrinhLab/CASPERpam
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https://github.com/mitmedialab/SPAMALOT
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CasLocusAnno/bin at master · RiversDong/CasLocusAnno
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CRISPRtrackBacterial species tracking
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CRISPRlong readsGenerating spacer graphs from CRISPR arrays predicted from long reads or other resources
https://www.frontiersin.org/articles/10.3389/fmicb.2019.02054/full
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Cas Orientation Direction of CRISPR-Cas arrayNo specific software
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