Benchmark datasets for testing AIRR-seq data processing with pyIgMap pipeline

This is a set of raw FASTQ files produced by various AIRR-seq protocols, stored here for benchmark conveinience and for reference purposes.

Currently it contains the following datasets:

id
fastq
reference
method
description

allergy

ERR7425614_1.fastq.gz,

ERR7425614_2.fastq.gz

https://doi.org/10.7554/eLife.79254
5'RACE, UMI, long MiSeq reads, IGH w/ isotype
Longitudinal full-length IGH repertoire profiling and clonal lineage dynamics in memory B cells, plasmablasts and plasma cells of human peripheral blood

covid

fmba_TRAB_R1.fastq.gz,

fmba_TRAB_R2.fastq.gz

https://doi.org/10.1101/2023.11.08.566227

DNA multiplex, UMI, TRA+TRB mix, NextSeq
TCR sequencing in COVID-19 convalescent and healthy donors

natprot

PMID27490633_R1.fastq.gz,

PMID27490633_R2.fastq.gz

https://doi.org/10.1038/nprot.2016.093

5'RACE, UMI, long MiSeq reads, high-quality overlap, IGH no isotype
High-quality full-length immunoglobulin profiling with unique molecular barcoding

brnaseq

SRR3743469_R1.fastq.gz,

SRR3743469_R2.fastq.gz

https://doi.org/10.1016/j.immuni.2016.08.012

RNA-Seq, all chains, B-cells
Primary human mature naïve B-cells (IgD+CD38lo; NB) and GCB-cells (CD77+CD38hi; GCB) were purified from tonsils of healthy individuals. RNA-seq libraries were prepared using the Illumina TruSeq RNA sample kits according to the manufacturer.

uhrr

UHRR_full_R1.fastq.gz,

UHRR_full_R2.fastq.gz

https://doi.org/10.1038/s41598-021-04583-z

RNA-Seq, bulk
Universal Human Reference RNA

10x

10x_bcr_R1.fastq.gz,

10x_bcr_R2.fastq.gz,

10x_tcr_R1.fastq.gz,

10x_tcr_R2.fastq.gz

https://www.10xgenomics.com/datasets/human-pbmc-from-a-healthy-donor-10-k-cells-v-2-2-standard-5-0-0

10x Genomics vdj
See reference. AIRR-seq is split into TCR and BCR parts