Table 1
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Summary of FLT3-ITD detection tools

ToolVersionLanguageDepended-upon packages and librariesInput formatOutput formatDetection strategy1HC data2Amplicon data2Variant typeYear publishedURL
Pindelv0.2.5b8C++htslibBAMVCFIYESYESIndels3 and SVs32009https://github.com/genome/pindel
ITDetectornull4Perlblat, bedtools, CAP3, fasta36, samtoolsBAMTSVIIYESNOonly ITDs2015https://github.com/ken0-1n/Genomon-ITDetector
BreaKmerv0.0.4-betaPythonblat, Cutadapt, JellyfishBAMTXTIIYESNOSVs2015https://github.com/ryanabo/BreaKmer
ITD AssemblernullHaskell, Python, Csamtools, bamtools, blastn, bedtools, phrap, GHC platformBAMBEDIIYESNOonly ITDs2015https://github.com/wudustan/ITD-Assembler
ITDseekv1.2PerlsamtoolsBAMVCFIYESYESonly ITDs2016https://github.com/tommyau/itdseek
getITDv1.2.2Pythonbiopython, easyguiFASTQTSVIYESYESonly ITDs2019https://github.com/tjblaette/getitd
ScanITDnullPythonsamtools, scikit-bio, pysamBAMVCFIYESYESonly ITDs2020https://github.com/ylab-hi/ScanITD
FLT3_ITD_extnullPerlsamtools, bwa, fgbio, bbmap, sumaclustBAM/FASTQVCFIYESYESonly ITDs2020https://github.com/ht50/FLT3_ITD_ext
ToolVersionLanguageDepended-upon packages and librariesInput formatOutput formatDetection strategy1HC data2Amplicon data2Variant typeYear publishedURL
Pindelv0.2.5b8C++htslibBAMVCFIYESYESIndels3 and SVs32009https://github.com/genome/pindel
ITDetectornull4Perlblat, bedtools, CAP3, fasta36, samtoolsBAMTSVIIYESNOonly ITDs2015https://github.com/ken0-1n/Genomon-ITDetector
BreaKmerv0.0.4-betaPythonblat, Cutadapt, JellyfishBAMTXTIIYESNOSVs2015https://github.com/ryanabo/BreaKmer
ITD AssemblernullHaskell, Python, Csamtools, bamtools, blastn, bedtools, phrap, GHC platformBAMBEDIIYESNOonly ITDs2015https://github.com/wudustan/ITD-Assembler
ITDseekv1.2PerlsamtoolsBAMVCFIYESYESonly ITDs2016https://github.com/tommyau/itdseek
getITDv1.2.2Pythonbiopython, easyguiFASTQTSVIYESYESonly ITDs2019https://github.com/tjblaette/getitd
ScanITDnullPythonsamtools, scikit-bio, pysamBAMVCFIYESYESonly ITDs2020https://github.com/ylab-hi/ScanITD
FLT3_ITD_extnullPerlsamtools, bwa, fgbio, bbmap, sumaclustBAM/FASTQVCFIYESYESonly ITDs2020https://github.com/ht50/FLT3_ITD_ext

1Two FLT3-ITD detection strategies include: strategy I ‘alignment information-based’ and strategy II ‘assembly-based’.

2The tool can detect FLT3-ITD using either hybridization capture (HC) or amplicon sequencing data.

3insertions and deletions (Indels); structural variants (SVs).

4GitHub does not include a version number.

Table 1
Open in new tab

Summary of FLT3-ITD detection tools

ToolVersionLanguageDepended-upon packages and librariesInput formatOutput formatDetection strategy1HC data2Amplicon data2Variant typeYear publishedURL
Pindelv0.2.5b8C++htslibBAMVCFIYESYESIndels3 and SVs32009https://github.com/genome/pindel
ITDetectornull4Perlblat, bedtools, CAP3, fasta36, samtoolsBAMTSVIIYESNOonly ITDs2015https://github.com/ken0-1n/Genomon-ITDetector
BreaKmerv0.0.4-betaPythonblat, Cutadapt, JellyfishBAMTXTIIYESNOSVs2015https://github.com/ryanabo/BreaKmer
ITD AssemblernullHaskell, Python, Csamtools, bamtools, blastn, bedtools, phrap, GHC platformBAMBEDIIYESNOonly ITDs2015https://github.com/wudustan/ITD-Assembler
ITDseekv1.2PerlsamtoolsBAMVCFIYESYESonly ITDs2016https://github.com/tommyau/itdseek
getITDv1.2.2Pythonbiopython, easyguiFASTQTSVIYESYESonly ITDs2019https://github.com/tjblaette/getitd
ScanITDnullPythonsamtools, scikit-bio, pysamBAMVCFIYESYESonly ITDs2020https://github.com/ylab-hi/ScanITD
FLT3_ITD_extnullPerlsamtools, bwa, fgbio, bbmap, sumaclustBAM/FASTQVCFIYESYESonly ITDs2020https://github.com/ht50/FLT3_ITD_ext
ToolVersionLanguageDepended-upon packages and librariesInput formatOutput formatDetection strategy1HC data2Amplicon data2Variant typeYear publishedURL
Pindelv0.2.5b8C++htslibBAMVCFIYESYESIndels3 and SVs32009https://github.com/genome/pindel
ITDetectornull4Perlblat, bedtools, CAP3, fasta36, samtoolsBAMTSVIIYESNOonly ITDs2015https://github.com/ken0-1n/Genomon-ITDetector
BreaKmerv0.0.4-betaPythonblat, Cutadapt, JellyfishBAMTXTIIYESNOSVs2015https://github.com/ryanabo/BreaKmer
ITD AssemblernullHaskell, Python, Csamtools, bamtools, blastn, bedtools, phrap, GHC platformBAMBEDIIYESNOonly ITDs2015https://github.com/wudustan/ITD-Assembler
ITDseekv1.2PerlsamtoolsBAMVCFIYESYESonly ITDs2016https://github.com/tommyau/itdseek
getITDv1.2.2Pythonbiopython, easyguiFASTQTSVIYESYESonly ITDs2019https://github.com/tjblaette/getitd
ScanITDnullPythonsamtools, scikit-bio, pysamBAMVCFIYESYESonly ITDs2020https://github.com/ylab-hi/ScanITD
FLT3_ITD_extnullPerlsamtools, bwa, fgbio, bbmap, sumaclustBAM/FASTQVCFIYESYESonly ITDs2020https://github.com/ht50/FLT3_ITD_ext

1Two FLT3-ITD detection strategies include: strategy I ‘alignment information-based’ and strategy II ‘assembly-based’.

2The tool can detect FLT3-ITD using either hybridization capture (HC) or amplicon sequencing data.

3insertions and deletions (Indels); structural variants (SVs).

4GitHub does not include a version number.

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