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scTCRseq specifications


Unique identifier OMICS_12346
Name scTCRseq
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Paired-end single-cell RNA-seq data
Operating system Unix/Linux
Programming languages Python
License GNU Affero General Public License version 3
Computer skills Advanced
Stability Stable
SEQTK, Blastall, GapFiller, Vidjil
Maintained Yes


No version available



  • person_outline David Redmond

scTCRseq citation


Single cell TCRseq: paired recovery of entire T cell alpha and beta chain transcripts in T cell receptors from single cell RNAseq

Genome Med
PMCID: 4962388
PMID: 27460926
DOI: 10.1186/s13073-016-0335-7

[…] Quality control was performed (“Methods” and Additional file : Table S1) and 71 samples were subsequently selected for processing in scTCRseq (with BLAST eValue threshold 1e-8, minimum supporting read coverage 5, and estimated mean insert size of 175). The reads were mapped in BLAST using the custom mice variable and constant gene […]

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