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Broad Institute Inc picard tools mark duplicate command line utility
Picard Tools Mark Duplicate Command Line Utility, supplied by Broad Institute Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/command+line+utility/picard+markduplicates+tool/10__17582_slash_journal__pjz_slash_20211221081250-55-7-18
Average 90 stars, based on 1 article reviews
picard tools mark duplicate command line utility - by Bioz Stars, 2026-11
90/100 stars

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other:

Article Title: A burden of rare copy number variants in obsessive-compulsive disorder
Article Snippet: In brief, the ‘gencall’ command in the Illumina command line utility (iaap-cli, v1.1.0-1.1.0sha.80d7e5b3d9c1fdfc2e99b472a90652fd3848bbc7) was used to produce GTC files for each dataset processed from input IDATs, BPM and EGT files, and the ‘gtc2vcf’ plugin for bcftools (version 2020-01-14 from https://github.com/freeseek/gtc2vcf) was used with the ‘—adjustclusters’ option turned to adjust cluster centers in a manner that is specific to each input dataset and produce BCF files with genotype calls and intensity values per dataset.

Sequencing:

Article Title: Challenges and considerations for whole-genome-based antimicrobial resistance plasmid investigations
Article Snippet: SeqSphere+ ( ) , 2024 , Real-time plasmid transmission detection pipeline based on Mash distance. Includes plasmid reconstruction and typing using MOB-suite. Users can visualize output on the same platform. Available as a desktop application. Accessible at: https://www.ridom.de/seqsphere/u/Long-read_Data_Plasmid_Transmission_Analysis_Module.html. .. National Center for Biotechnology Information (NCBI) , N/A , NCBI nucleotide database for general genome sequence queries and download. Users can restrict search to “Genetic compartments: Plasmid” for the desired species or genus. Command line utility ( ncbi-genome-download ) available to download sequences with customizable parameters. Accessible at: https://www.ncbi.nlm.nih.gov/nucleotide/. .. PLSDB ( , ) , 2019 , Open access database containing plasmid sequences retrieved from NCBI Nucleotide. Sequence metadata is available for download. Users can upload their own plasmid FASTA sequence and search for similar matches using the BLAST utility. Metadata filtering is available. The database was last updated on 31 May 2024. Accessible at: https://ccb-microbe.cs.uni-saarland.de/plsdb/.

Plasmid Preparation:

Article Title: Challenges and considerations for whole-genome-based antimicrobial resistance plasmid investigations
Article Snippet: SeqSphere+ ( ) , 2024 , Real-time plasmid transmission detection pipeline based on Mash distance. Includes plasmid reconstruction and typing using MOB-suite. Users can visualize output on the same platform. Available as a desktop application. Accessible at: https://www.ridom.de/seqsphere/u/Long-read_Data_Plasmid_Transmission_Analysis_Module.html. .. National Center for Biotechnology Information (NCBI) , N/A , NCBI nucleotide database for general genome sequence queries and download. Users can restrict search to “Genetic compartments: Plasmid” for the desired species or genus. Command line utility ( ncbi-genome-download ) available to download sequences with customizable parameters. Accessible at: https://www.ncbi.nlm.nih.gov/nucleotide/. .. PLSDB ( , ) , 2019 , Open access database containing plasmid sequences retrieved from NCBI Nucleotide. Sequence metadata is available for download. Users can upload their own plasmid FASTA sequence and search for similar matches using the BLAST utility. Metadata filtering is available. The database was last updated on 31 May 2024. Accessible at: https://ccb-microbe.cs.uni-saarland.de/plsdb/.



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