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. 2023 Jun 17;26(7):107171. doi: 10.1016/j.isci.2023.107171
REAGENT or RESOURCE SOURCE IDENTIFIER
Software and algorithms
VNtyper This paper https://github.com/hassansaei/VNtyper
Kestrel version 1.0.1 Audano, P.A. et al.21 https://github.com/paudano/kestrel
Code-adVNTR version 1.3.3 Park, J. et al.19 https://github.com/mehrdadbakhtiari/adVNTR
GATK version 4.2.5 McKenna, A. et al.35 https://gatk.broadinstitute.org/hc/en-us
BWA version v0.7.17-r1188 Li, H. et al.36 https://bio-bwa.sourceforge.net/
Sambamba version 0.6.8 Tarasov, A. et al.37 https://lomereiter.github.io/sambamba/
Samtools version 1.11 Li, H. et al.38 http://www.htslib.org/
Fastp version 0.23.2 Chen, S. et al.39 https://github.com/OpenGene/fastp
IGV version 2.16.1 Robinson, J.T. et al.22 https://software.broadinstitute.org/software/igv/
Python versions 3.9 and 2.7 Python Software Foundation https://www.python.org
Java version 8 Orcale https://www.java.com/en/
Critical commercial assays
SureSelectXT Reagent kits Agilent #G9642C
Twist Library Preparation kit Twist Bioscience #100572
Twist Hybridization and wash Kit Twist Bioscience #101025
SNaPshot Multiplexing kit ThermoFisher Scientific #4323159
MwoI restriction enzyme New England BioLabs #R0573
ExoSAP_ITTM ThermoFisher Scientific #78201
Ampure XP beads Beckman Coulter #A63882
BigDyeTM Terminator v3.1 Cycle Sequencing Kit ThermoFisher Scientific #4337456
Deposited data
Read-name replaced Bam files from MUC1 dupC positive patients This paper https://github.com/hassansaei/VNtyper
1000 Genomes high coverage Project Byrska-Bishop, M. et al.24 https://www.internationalgenome.org/data-portal/data-collection/30x-grch38
Oligonucleotides
SNaPshot amplification primer forward: actgtaaa
acgacggccagtCTGGGAATCGCACCAGCGTGTG
GCCCCGGGCTCCACC		 This paper N/A
SNaPshot amplification primer reverse-Fluo: accag
gaaacagctatgaccCGTGGATGAGGAGCCGCAGTG
TCCGGGGCCGAGGTGACA		 This paper N/A
Prob 7C:
CGGGCTCCACCGCCCCCCC		 This paper N/A
Prob 8C: gagagagagaCGGGCTCCACCGCCC
CCCCc		 This paper N/A
Other
3500 Genetic Analyzer ThermoFisher scientific #4406017
NextSeq 500 sequencer Illumina https://emea.illumina.com/systems/sequencing-platforms/nextseq.html
MiSeq sequencers Illumina https://emea.illumina.com/systems/sequencing-platforms/nextseq.html