Benchmark datasets for testing AIRR-seq data processing with pyIgMap pipeline
Authors/Creators
Description
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 |
Files
Files
(16.3 GB)
| Name | Size | |
|---|---|---|
|
md5:9e3a789de18303abdf1e40aa5b51e41a
|
773.9 MB | Download |
|
md5:a311561e9847531654f4cad23a990300
|
1.9 GB | Download |
|
md5:21e14ac69c30824e14dc2cdc1ef496cb
|
746.0 MB | Download |
|
md5:6067cded830315a47a2b3d240bacbf19
|
1.6 GB | Download |
|
md5:a1bccc3651f6619e8c112957ec5fcb28
|
441.8 MB | Download |
|
md5:b8935387579db3a8dfa8675458bc90e9
|
514.7 MB | Download |
|
md5:bb2de0439ea6bcdc3073a636b8891ca1
|
465.1 MB | Download |
|
md5:04cf39c505f5f9fc69aa600a6262f5d0
|
188.8 MB | Download |
|
md5:354436932f2155ed42924e928ba0b0b3
|
313.3 MB | Download |
|
md5:00f655b6d176abe7d4bc5c583b5b01fc
|
344.0 MB | Download |
|
md5:6d05f9aa74890ca11cb7984271ea35f3
|
1.4 GB | Download |
|
md5:ac3970258f05d416bbce31490919957b
|
1.4 GB | Download |
|
md5:2228f6ee544ea1b2b231133fee06dc51
|
3.0 GB | Download |
|
md5:311efc349f74bd4fa139c083e6512135
|
3.1 GB | Download |