TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data

We introduce the TRUST4 open-source algorithm for reconstructing immune receptor repertoires in αβ/γδ T-cells and B-cells from RNA-seq data. Compared to competing methods, TRUST4 supports both FASTQ and BAM formats, is faster and more sensitive in assembling longer, even full-length, receptor repert...

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Detalles Bibliográficos
Autores principales: Song, Li, Cohen, David, Ouyang, Zhangyi, Cao, Yang, Hu, Xihao, Liu, X. Shirley
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2021
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9328942/
https://www.ncbi.nlm.nih.gov/pubmed/33986545
http://dx.doi.org/10.1038/s41592-021-01142-2
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author Song, Li
Cohen, David
Ouyang, Zhangyi
Cao, Yang
Hu, Xihao
Liu, X. Shirley
author_facet Song, Li
Cohen, David
Ouyang, Zhangyi
Cao, Yang
Hu, Xihao
Liu, X. Shirley
author_sort Song, Li
collection PubMed
description We introduce the TRUST4 open-source algorithm for reconstructing immune receptor repertoires in αβ/γδ T-cells and B-cells from RNA-seq data. Compared to competing methods, TRUST4 supports both FASTQ and BAM formats, is faster and more sensitive in assembling longer, even full-length, receptor repertoires. TRUST4 can also call repertoire sequences from single-cell RNA-seq (scRNA-seq) data without V(D)J enrichment, and is compatible with both SMART-seq and 5’ 10X Genomics platforms.
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spelling pubmed-93289422022-07-27 TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data Song, Li Cohen, David Ouyang, Zhangyi Cao, Yang Hu, Xihao Liu, X. Shirley Nat Methods Article We introduce the TRUST4 open-source algorithm for reconstructing immune receptor repertoires in αβ/γδ T-cells and B-cells from RNA-seq data. Compared to competing methods, TRUST4 supports both FASTQ and BAM formats, is faster and more sensitive in assembling longer, even full-length, receptor repertoires. TRUST4 can also call repertoire sequences from single-cell RNA-seq (scRNA-seq) data without V(D)J enrichment, and is compatible with both SMART-seq and 5’ 10X Genomics platforms. 2021-06 2021-05-13 /pmc/articles/PMC9328942/ /pubmed/33986545 http://dx.doi.org/10.1038/s41592-021-01142-2 Text en http://www.nature.com/authors/editorial_policies/license.html#termsUsers may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Song, Li
Cohen, David
Ouyang, Zhangyi
Cao, Yang
Hu, Xihao
Liu, X. Shirley
TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data
title TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data
title_full TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data
title_fullStr TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data
title_full_unstemmed TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data
title_short TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data
title_sort trust4: immune repertoire reconstruction from bulk and single-cell rna-seq data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9328942/
https://www.ncbi.nlm.nih.gov/pubmed/33986545
http://dx.doi.org/10.1038/s41592-021-01142-2
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