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Old 05-04-2019, 02:09 AM   #1
ekarais
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Location: Europe

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Question Obtaining the chemistry used from the samfile

Hello everyone,

I have some Ecoli reads (PacBio RS) in SAM format, and I want to figure out the specific chemistry used (P6-C4, P4-C2, etc.)

From this link: https://bioinformatics.stackexchange...equel-bams-hea

I found out that I could check the BASECALLERVERSION field under @RG in the SAM file. For these reads, the BASECALLERVERSION is 2.3.0.0.140640

What is the corresponding chemistry?
More generally, is there list that gives this information for all basecaller versions?
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Old 05-04-2019, 05:40 AM   #2
michaeletoler
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Nice question. I also like to know.
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Old 05-04-2019, 07:48 PM   #3
SNPsaurus
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The source code for pbbam (https://github.com/PacificBioscience...istryTable.cpp) has this table, which says that the 2.3 basecaller is for the P6-C4 chemistry.
// BindingKit, SequencingKit, BasecallerVersion, Chemistry

// RS
{{"100356300", "100356200", "2.1", "P6-C4"}},
{{"100356300", "100356200", "2.3", "P6-C4"}},
{{"100356300", "100612400", "2.1", "P6-C4"}},
{{"100356300", "100612400", "2.3", "P6-C4"}},
{{"100372700", "100356200", "2.1", "P6-C4"}},
{{"100372700", "100356200", "2.3", "P6-C4"}},
{{"100372700", "100612400", "2.1", "P6-C4"}},
{{"100372700", "100612400", "2.3", "P6-C4"}},

// 3.0 ("Dromedary"): S/P1-C1/beta
{{"100-619-300", "100-620-000", "3.0", "S/P1-C1/beta"}},
{{"100-619-300", "100-620-000", "3.1", "S/P1-C1/beta"}},

// 3.1 ("Echidna"): S/P1-C1.1
{{"100-619-300", "100-867-300", "3.1", "S/P1-C1.1"}},
{{"100-619-300", "100-867-300", "3.2", "S/P1-C1.1"}},
{{"100-619-300", "100-867-300", "3.3", "S/P1-C1.1"}},

// 3.1.1 ("Flea"): S/P1-C1.2
{{"100-619-300", "100-902-100", "3.1", "S/P1-C1.2"}},
{{"100-619-300", "100-902-100", "3.2", "S/P1-C1.2"}},
{{"100-619-300", "100-902-100", "3.3", "S/P1-C1.2"}},
{{"100-619-300", "100-902-100", "4.0", "S/P1-C1.2"}},
{{"100-619-300", "100-902-100", "4.1", "S/P1-C1.2"}},

// 3.2 ("Goat"): S/P1-C1.3
{{"100-619-300", "100-972-200", "3.2", "S/P1-C1.3"}},
{{"100-619-300", "100-972-200", "3.3", "S/P1-C1.3"}},
{{"100-619-300", "100-972-200", "4.0", "S/P1-C1.3"}},
{{"100-619-300", "100-972-200", "4.1", "S/P1-C1.3"}},

// 4.0 ("Seabiscuit"); S/P2-C2
{{"100-862-200", "100-861-800", "4.0", "S/P2-C2"}},
{{"100-862-200", "100-861-800", "4.1", "S/P2-C2"}},
{{"100-862-200", "101-093-700", "4.1", "S/P2-C2"}},

// 5.0 ("Iguana"); S/P2-C2
{{"100-862-200", "100-861-800", "5.0", "S/P2-C2/5.0"}},
{{"100-862-200", "101-093-700", "5.0", "S/P2-C2/5.0"}},

// 5.0.1 ChemRel ("Sequel® Sequencing Plate Silwet"); S/P2-C2
{{"100-862-200", "101-309-500", "5.0", "S/P2-C2/5.0"}},
// 5.0.1 ChemRel ("Sequel® Sequencing Plate Silwet (4 rxn)"); S/P2-C2
{{"100-862-200", "101-309-400", "5.0", "S/P2-C2/5.0"}},

// --- SG1/16509P/PA5.0 ---
// 2.1 binding kit/5.1PA support with ..
// 5.0 ("Iguana"); S/P2-C2
{{"101-365-900", "100-861-800", "5.0", "S/P2-C2/5.0"}},
{{"101-365-900", "101-093-700", "5.0", "S/P2-C2/5.0"}},

// 5.0.1 ChemRel; Sequel® Binding Kit 2.1; S/P2-C2
{{"101-365-900", "101-309-500", "5.0", "S/P2-C2/5.0"}}, // Sequel® Sequencing Plate 2.1 Silwet (8 rxn)
{{"101-365-900", "101-309-400", "5.0", "S/P2-C2/5.0"}}, // Sequel® Sequencing Plate 2.1 Silwet (4 rxn)

// 5.0.1 ChemRel; Sequel® Binding Kit 3.0; S/P3-C3
{{"101-500-400", "101-427-500", "5.0", "S/P3-C3/5.0"}}, // Sequel® Sequencing Plate 3.0 (8 rxn)
{{"101-500-400", "101-427-800", "5.0", "S/P3-C3/5.0"}}, // Sequel® Sequencing Plate 3.0 (4 rxn)

// 5.0.1 ChemRel; Sequel® Dev Binding Kit; S/P2-C2
{{"101-490-800", "101-490-900", "5.0", "S/P3-C1/5.0-8M"}}, // Sequel II® Sequencing Plate (4 rxn)
{{"101-490-800", "101-491-000", "5.0", "S/P3-C1/5.0-8M"}}, // Sequel II® Sequencing Plate (8 rxn)

// 5.0.1 ChemRel; Sequel® Sequencing Plate 3.1 for Dynamic Loading placeholder (4 rxn)
{{"101-500-400", "101-646-800", "5.0", "S/P3-C3/5.0"}}, // Sequel® Sequencing Plate 3.1 for Dynamic Loading placeholder

// 5.0.1 ChemRel; Sequel® Dev Sequencing Plate Dyn Loading (4 rxn)
{{"101-490-800", "101-644-500", "5.0", "S/P3-C1/5.0-8M"}}, // Sequel® Dev Sequencing Plate Dyn Loading

// 5.0.1 ChemRel; Sequel® Sequencing Plate Dyn Loading (4 rxn)
{{"101-490-800", "101-717-100", "5.0", "S/P3-C1/5.0-8M"}}, // Sequel® Dev Sequencing Plate Dyn Loading

// 5.0.1 ChemRel; Sequel® Dev Sequencing Plate Dyn Loading (4 rxn)
{{"101-717-300", "101-644-500", "5.0", "S/P3-C1/5.0-8M"}}, // Sequel® Dev Sequencing Plate Dyn Loading
// 5.0.1 ChemRel; Sequel® Sequencing Plate Dyn Loading (4 rxn)
{{"101-717-300", "101-717-100", "5.0", "S/P3-C1/5.0-8M"}}, // Sequel® Dev Sequencing Plate Dyn Loading

// 5.0.1 ChemRel; Sequel® Dev Sequencing Plate Dyn Loading (4 rxn)
{{"101-717-400", "101-644-500", "5.0", "S/P3-C1/5.0-8M"}}, // Sequel® Dev Sequencing Plate Dyn Loading
// 5.0.1 ChemRel; Sequel® Sequencing Plate Dyn Loading (4 rxn)
{{"101-717-400", "101-717-100", "5.0", "S/P3-C1/5.0-8M"}} // Sequel® Dev Sequencing Plate Dyn Loading
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