assemblePartial report
MiXCR generates a comprehensive summary of partial assembly performance. Assemble reports may be generated right along with assemblePartial command using -r/--report for txt report and -j/--json-report for report in a json format, or can be exported using exportReports command.
Show sample report
============== AssemblePartial Report ============== Analysis date: Thu Jul 28 11:51:13 CEST 2022 Input file(s): clones_newMiXcr/Donor1_MBC_2010_corrected.vdjca Output file(s): clones_newMiXcr/Donor1_MBC_2010_partialAssemble.vdjca Version: ; built=Fri Jul 15 01:51:38 CEST 2022; rev=aa769be87b; lib=repseqio.v2.0 Command line arguments: assemblePartial -f --report clones_newMiXcr/Donor1_MBC_2010_assemblePartialReport.txt -j clones_newMiXcr/Donor1_MBC_2010_assemblePartialReport.json clones_newMiXcr/Donor1_MBC_2010_corrected.vdjca clones_newMiXcr/Donor1_MBC_2010_partialAssemble.vdjca Analysis time: 12.71m Independent runs: 118472787 Total alignments analysed: 118472787 Number of output alignments: 118169463 (99.74%) Alignments already with CDR3 (no overlapping is performed): 5420162 (4.58%) Successfully overlapped alignments: 302715 (0.26%) Left parts with too small N-region (failed to extract k-mer): 4530050 (3.82%) Extracted k-mer diversity: 19607617 Dropped due to wildcard in k-mer: 0 (0%) Dropped due to too short NRegion parts in overlap: 51841 (0.04%) Dropped overlaps with empty N region due to no complete NDN coverage: 3958 (0%) Number of left-side alignments: 1835970 (1.55%) Number of right-side alignments: 3167157 (2.67%) Complex overlaps: 0 (0%) Over-overlaps: 197 (0%) Partial alignments written to output: 112446586 (94.91%)
json { "type": "partialAlignmentsAssemblerReport", "commandLine": "assemblePartial -f --report clones_newMiXcr/Donor1_MBC_2010_assemblePartialReport.txt -j clones_newMiXcr/Donor1_MBC_2010_assemblePartialReport.json clones_newMiXcr/Donor1_MBC_2010_corrected.vdjca clones_newMiXcr/Donor1_MBC_2010_partialAssemble.vdjca", "inputFiles": [ "clones_newMiXcr/Donor1_MBC_2010_corrected.vdjca" ], "outputFiles": [ "clones_newMiXcr/Donor1_MBC_2010_partialAssemble.vdjca" ], "version": "; built=Fri Jul 15 01:51:38 CEST 2022; rev=aa769be87b; lib=repseqio.v2.0", "independentRuns": 6478545, "totalProcessed": 118472787, "outputAlignments": 118169463, "withCDR3": 5420162, "overlapped": 302715, "leftTooShortNRegion": 4530050, "kMerDiversity": 19607617, "droppedWildcardsInKMer": 0, "droppedSmallOverlapNRegion": 51841, "droppedNoNRegion": 3958, "leftParts": 1835970, "rightParts": 3167157, "complexOverlaps": 0, "overOverlaps": 197, "partialAlignmentsAsIs": 112446586 }
Independent runs- Number of independent
assemblePartialrounds Total alignments analysed- Number of total input alignments
Number of output alignments- Number of total output alignments
Alignments already with CDR3 (no overlapping is performed)- Number of input alignments that already covered
CDR3 Successfully overlapped alignments- Number of overlapped alignments
Left parts with too small N-region (failed to extract k-mer)- Number of left alignments with too small N-region (not enough entropy to assign to a unique molecule)
Extracted k-mer diversity- Number of different k-mers
Dropped due to wildcard in k-mer- Dropped alignments due wildcards in k-mers
Dropped due to too short NRegion parts in overlap- Dropped due too small number of N letters in overlap (not enough entropy to assign to a unique molecule)
Dropped overlaps with empty N region due to no complete NDN coverage- Dropped due absent N letters in overlap (not enough entropy to assign to a unique molecule)
Number of left-side alignments- Number of left alignments
Number of right-side alignments- Number of right alignments
Complex overlaps- Multiple overlaps for same molecule
Over-overlaps- Over overlaped alignments
Partial alignments written to output- Partial (no full CDR3) alignments written to output