Datasets:

isalgo
/

airr_benchmark

text stringlengths 54 2.11M
count freq cdr3nt cdr3aa v d j VEnd DStart DEnd JStart
32191 0.03576809571640637 TGTGCCAGCAGCTTAGTCTCTGGGGCCAACGTCCTGACTTTC CASSLVSGANVLTF TRBV7-9 . TRBJ2-6 16 -40 -40 17
21204 0.02356020942408377 TGTGCCAGCAGCGACCCCCAGAGCTCCTATAATTCACCCCTCCACTTT CASSDPQSSYNSPLHF TRBV7-8 TRBD1 TRBJ1-6 12 14 19 20
8530 0.009477862025440226 TGTGCCATCGGGACAGGCGATAGCAATCAGCCCCAGCATTTT CAIGTGDSNQPQHF TRBV10-3 TRBD1 TRBJ1-5 9 9 16 16
7293 0.008103405363603232 TGTGCCAGCCTTGGAGGCAGGAGCTCCTATAATTCACCCCTCCACTTT CASLGGRSSYNSPLHF TRBV6-5 TRBD2 TRBJ1-6 9 12 17 18
4969 0.005521160188090561 TGTGCCAGCAGTTTAGGTGTCGGAACCTACGAGCAGTACTTC CASSLGVGTYEQYF TRBV27 . TRBJ2-7 15 -40 -40 25
4030 0.004477817580600716 TGTGCCAGCAGCTCCCGATTCGGGGAAAAGGTGGAGACCCAGTACTTC CASSSRFGEKVETQYF TRBV13 . TRBJ2-5 13 -34 -34 33
3740 0.0041555924941555035 TGTGCCAGCAGGGAGGGGTCGAACACCGGGGAGCTGTTTTTT CASREGSNTGELFF TRBV3-2 TRBD2 TRBJ2-2 11 11 17 19
3729 0.00414337016329034 TGTGCAGGGTCGGACGAGAGCTCCTACAATGAGCAGTTCTTC CAGSDESSYNEQFF TRBV6-1 . TRBJ2-1 5 -40 -40 17
3239 0.0035989208792967047 TGTGCCAGCAGCCCTGAGACTGAAGCTTTCTTT CASSPETEAFF TRBV7-9 . TRBJ1-1 12 -49 -49 18
3157 0.0035078089583018518 TGTGCCTGGAGTGTACAGTGGGGAGGTGGGCACACAGATACGCAGTATTTT CAWSVQWGGGHTDTQYF TRBV30 TRBD2 TRBJ2-3 17 20 26 32
3132 0.0034800309336082986 TGCGCCAGCAGCCAAACTCGGACAGGGAATCTAGCCAAAAACATTCAGTACTTC CASSQTRTGNLAKNIQYF TRBV4-3 TRBD1 TRBJ2-4 15 19 27 30
2951 0.0032789180348269764 TGCGCCAGCAGCCAAGTAGGGATGTCTGAAGCTTTCTTT CASSQVGMSEAFF TRBV4-1 . TRBJ1-1 16 -43 -43 25
2830 0.0031444723953101806 TGTGCCAGCAGTGAACGGGAGAACACTGAAGCTTTCTTT CASSERENTEAFF TRBV6-1 TRBD2 TRBJ1-1 15 15 20 20
2822 0.0031355834274082437 TGTGCCAGTTCTTTTACCCCGGGACAATGGTGGACAGATACGCAGTATTTT CASSFTPGQWWTDTQYF TRBV6-6 TRBD1 TRBJ2-3 8 17 26 33
2719 0.003021137965670806 TGCGCCAGCAGCCAGTACGGGGGTCCTAGCTCCTACAATGAGCAGTTCTTC CASSQYGGPSSYNEQFF TRBV4-1 TRBD1 TRBJ2-1 14 18 23 27
2638 0.002931137165663695 TGCGCCAGCAGCTTGATTTATGGGGGCGCGGGGAACACTGAAGCTTTCTTT CASSLIYGGAGNTEAFF TRBV5-1 TRBD1 TRBJ1-1 15 21 29 32
2439 0.002710024089103014 TGTGCCATCGGAACAGGAGATAGCAATCAGCCCCAGCATTTT CAIGTGDSNQPQHF TRBV10-3 TRBD1 TRBJ1-5 9 9 17 19
2345 0.0026055787162552555 TGTGCCAGCAGTGAAGAGGAAGGACAGGGTTCCTACGAGCAGTACTTC CASSEEEGQGSYEQYF TRBV6-1 TRBD1 TRBJ2-7 16 21 29 30
2338 0.002597800869341061 TGTGCCAGCAGCTTAGCTGGAAGGGCGCGAAATCAGCCCCAGCATTTT CASSLAGRARNQPQHF TRBV11-2 TRBD1 TRBJ1-5 16 22 28 30
1992 0.0022133530075822898 TGTGCCAGCAGCCAGGGGCCAGGGCGGGCCACTGAAGCTTTCTTT CASSQGPGRATEAFF TRBV7-9 TRBD1 TRBJ1-1 12 15 24 29
1942 0.002157796958195184 TGTGCCAGCGTCTCCGGGACAGGGAGGGGCTATGGCTACACCTTC CASVSGTGRGYGYTF TRBV2 TRBD1 TRBJ1-2 9 9 24 29
1941 0.002156685837207442 TGCGCCAGCAGCCACCTCGACTGGAACACTGAAGCTTTCTTT CASSHLDWNTEAFF TRBV4-1 . TRBJ1-1 14 -40 -40 23
1886 0.0020955741828816254 TGTGCCACCGGGACAGGAGATAGCAATCAGCCCCAGCATTTT CATGTGDSNQPQHF TRBV10-3 TRBD1 TRBJ1-5 7 7 17 19
1847 0.0020522404643596834 TGTGCCTGGAGTGTTTACGATGGCTACACCTTC CAWSVYDGYTF TRBV30 . TRBJ1-2 14 -49 -49 16
1805 0.0020055733828745143 TGTGCCATCAGCACAGGGGATAGCAATCAGCCCCAGCATTTT CAISTGDSNQPQHF TRBV10-3 TRBD1 TRBJ1-5 11 12 19 19
1769 0.0019655730273157985 TGTGCCAGCAGTTCGGGCGGTAGCAATCAGCCCCAGCATTTT CASSSGGSNQPQHF TRBV6-3 TRBD1 TRBJ1-5 13 14 19 20
1761 0.0019566840594138616 TGTGCCACTTCGACAGGGGATAGCAATCAGCCCCAGCATTTT CATSTGDSNQPQHF TRBV10-3 TRBD1 TRBJ1-5 7 11 19 19
1747 0.001941128365585472 TGTGCCAGCAGTTACGCGGTGGGGGATTGGGCCTACAATGAGCAGTTCTTC CASSYAVGDWAYNEQFF TRBV6-6 TRBD1 TRBJ2-1 18 20 25 31
1722 0.001913350340891919 TGTGCCAGCAGTTTGTCTGACGTGCCGGGGCAAATTAGTACACCCCTCCACTTT CASSLSDVPGQISTPLHF TRBV12-4 TRBD1 TRBJ1-6 14 21 32 40
1694 0.00188223895323514 TGTGCCAGCAGTTTTCTGGCAGCGAACACTGAAGCTTTCTTT CASSFLAANTEAFF TRBV12-4 . TRBJ1-1 14 -40 -40 23
1661 0.0018455719606396501 TGTGCCAGTACCCCAGGGGAACCCTCTGGGGCCAACGTCCTGACTTTC CASTPGEPSGANVLTF TRBV19 TRBD1 TRBJ2-6 10 13 19 23
1540 0.0017111263211228545 TGTGCCAGCAGCGTAGGGCCAGGGGAGTACATGAACACTGAAGCTTTCTTT CASSVGPGEYMNTEAFF TRBV9 TRBD1 TRBJ1-1 16 16 25 26
1519 0.00168779278038027 TGTGCCAGCAGCTTAGGGGCAGGGGACGAGCAGTACTTC CASSLGAGDEQYF TRBV7-6 TRBD1 TRBJ2-7 16 16 25 25
1513 0.0016811260544538173 TGTGCCAGCAGGGGAGTCGGACAGGGCAACATAAACTATGGCTACACCTTC CASRGVGQGNINYGYTF TRBV6-6 TRBD1 TRBJ1-2 11 18 26 33
1499 0.0016655703606254279 TGTGCCAGCAGCCCCCGGACAGGGTATGGGACTGAAGCTTTCTTT CASSPRTGYGTEAFF TRBV28 TRBD1 TRBJ1-1 11 12 24 30
1472 0.0016355700939563907 TGCGCCAGCAGCCTCCAGCCGGGTACTTTCACAGATACGCAGTATTTT CASSLQPGTFTDTQYF TRBV5-1 TRBD2 TRBJ2-3 12 18 27 29
1427 0.0015855696495079956 TGTGCCAGCAGTTACTCGGGGCGCCGTAACACTGAAGCTTTCTTT CASSYSGRRNTEAFF TRBV6-5 TRBD1 TRBJ1-1 18 18 25 27
1398 0.0015533471408634744 TGTGCCACCTCGACAGGGGACAGCAATCAGCCCCAGCATTTT CATSTGDSNQPQHF TRBV10-3 TRBD1 TRBJ1-5 7 11 19 21
1372 0.0015244579951821794 TGCGCCAGCAGCTTGGATTTTGGGACAGGGTACGAGCAGTACTTC CASSLDFGTGYEQYF TRBV5-1 TRBD1 TRBJ2-7 16 21 30 30
1293 0.0014366794371505525 TGTGCCAGCAGTTTGGGGTACGAGCAGTACTTC CASSLGYEQYF TRBV12-4 . TRBJ2-7 14 -49 -49 18
1183 0.00131445612849892 TGTGCCAGCAGTCGGACAGGGGGTGGGGACGAGCAGTACTTC CASSRTGGGDEQYF TRBV7-9 TRBD1 TRBJ2-7 11 13 23 28
1141 0.0012677890470137513 TGTGCCAGCAGCCTCAATTCTGAAGCTTTCTTT CASSLNSEAFF TRBV11-2 . TRBJ1-1 12 -49 -49 19
1126 0.0012511222321976195 TGTGCCAGCAGCTACCTCGGGTTACAGATCTACGAGCAGTACTTC CASSYLGLQIYEQYF TRBV12-4 . TRBJ2-7 11 -37 -37 29
1114 0.0012377887803447143 TGTGCCAGTAGTACAGGGGATAGCAATCAGCCCCAGCATTTT CASSTGDSNQPQHF TRBV19 . TRBJ1-5 16 -40 -40 19
1088 0.0012088996346634193 TGTGCCATCGGAACAGGGGATAGCAATCAGCCCCAGCATTTT CAIGTGDSNQPQHF TRBV10-3 TRBD1 TRBJ1-5 9 9 19 19
1053 0.0011700104000924453 TGTGCCAGCAGCTGGCTAGGGACAGTACTCCATGAGCAGTTCTTC CASSWLGTVLHEQFF TRBV7-9 TRBD1 TRBJ2-1 13 18 25 31
1034 0.0011488991013253451 TGTGCCATAGGGACAGGTGATAGCAATCAGCCCCAGCATTTT CAIGTGDSNQPQHF TRBV10-3 TRBD1 TRBJ1-5 8 9 17 19
1008 0.0011200099556440502 TGCAGCGTGTCACAGGGGGACGGAACTGAAGCTTTCTTT CSVSQGDGTEAFF TRBV29-1 TRBD1 TRBJ1-1 8 11 19 24
989 0.00109889865687695 TGTGCCAGTAGTCTCAGCTTGGACACCGGGGAGCTGTTTTTT CASSLSLDTGELFF TRBV19 . TRBJ2-2 12 -40 -40 22
981 0.0010900096889750132 TGTGCCAGCTCCCCTCTTTCGGTGAACACTGAAGCTTTCTTT CASSPLSVNTEAFF TRBV12-4 TRBD2 TRBJ1-1 9 10 15 22
952 0.0010577871803304918 TGTGCCAGCAGCCAATACGAGGGGGGTGAAGCTTTCTTT CASSQYEGGEAFF TRBV7-9 TRBD1 TRBJ1-1 12 19 25 26
912 0.0010133423408208073 TGCGCCAGCAGCTTGTTGGGGCAGGGGGACGAGCAGTACTTC CASSLLGQGDEQYF TRBV5-1 TRBD1 TRBJ2-7 15 17 28 28
911 0.001012231219833065 TGTGCCAGCAGTGACTCGGGAGACGGCACAGATACGCAGTATTTT CASSDSGDGTDTQYF TRBV6-4 . TRBJ2-3 18 -37 -37 25
895 9.944532840291914E-4 TGTGCCAGCAGTCCTGCTAGCGGGGTACCTCTCGAGCAGTACTTC CASSPASGVPLEQYF TRBV6-1 TRBD2 TRBJ2-7 12 16 24 32
882 9.80008711188544E-4 TGTGCCAGCAGCCCGGAGGGGTTGGGCACTGAAGCTTTCTTT CASSPEGLGTEAFF TRBV12-4 TRBD2 TRBJ1-1 11 14 20 26
862 9.577862914337017E-4 TGTGCCAGCAGTCCGGGAGGGGAGGAAAAACTGTTTTTT CASSPGGEEKLFF TRBV2 TRBD2 TRBJ1-4 12 13 21 24
859 9.544529284704753E-4 TGTGCCAGCACCGGGCCGGGTTGGGGTACGCAGTATTTT CASTGPGWGTQYF TRBV28 TRBD2 TRBJ2-3 10 10 15 26
847 9.4111947661757E-4 TGCGCCAGCAGCTTTCGACAGGGCCCGGCTAATTCACCCCTCCACTTT CASSFRQGPANSPLHF TRBV5-1 TRBD2 TRBJ1-6 14 16 23 29
829 9.211192988382119E-4 TGTGCCAGCAAGCCGCCCGGGGCCAACGTCCTGACTTTC CASKPPGANVLTF TRBV28 TRBD1 TRBJ2-6 10 13 18 18
795 8.8334118525498E-4 TGTGCCAGTGGCACTGGGGATAGCAATCAGCCCCAGCATTTT CASGTGDSNQPQHF TRBV19 . TRBJ1-5 9 -40 -40 19
780 8.666743704388483E-4 TGTGCCAGCAGTTTCAAGGATCCTAGCGCTCAGTACTTC CASSFKDPSAQYF TRBV12-4 TRBD2 TRBJ2-5 14 22 28 30
777 8.63341007475622E-4 TGTGCCAGCAACGATCCCTTAAGCTCCTATAATTCACCCCTCCACTTT CASNDPLSSYNSPLHF TRBV6-5 . TRBJ1-6 10 -34 -34 21
775 8.611187655001378E-4 TGTGCCAGCAGTTTAGTCTTCCAAACTTATAGCAATCAGCCCCAGCATTTT CASSLVFQTYSNQPQHF TRBV12-4 . TRBJ1-5 16 -31 -31 27
763 8.477853136472324E-4 TGTGCCAGCAGACCGGGACAGGGCCACGAGCAGTACTTC CASRPGQGHEQYF TRBV6-3 TRBD1 TRBJ2-7 11 12 23 25
755 8.388963457452956E-4 TGTGCCAGCAGTCTATTGGGACGGACTAGCACAGATACGCAGTATTTT CASSLLGRTSTDTQYF TRBV12-4 TRBD2 TRBJ2-3 15 17 22 25
744 8.266740148801323E-4 TGTGCCAGCAGTGACGGGCCACTGACTGAAGCTTTCTTT CASSDGPLTEAFF TRBV6-4 TRBD2 TRBJ1-1 15 15 20 24
699 7.766735704317372E-4 TGTGCCAGCAGCTTAACCCCCGAACATGAGCAGTTCTTC CASSLTPEHEQFF TRBV7-2 TRBD1 TRBJ2-1 15 16 21 25
681 7.566733926523792E-4 TGTGCCAGCTCCACAGGAGATAGCAATCAGCCCCAGCATTTT CASSTGDSNQPQHF TRBV19 TRBD1 TRBJ1-5 8 12 17 19
664 7.377843358607633E-4 TGTGCCAGCAGTGAATCCGTCCGGGGTGAAAAACTGTTTTTT CASSESVRGEKLFF TRBV6-1 TRBD2 TRBJ1-4 15 18 26 26
642 7.133396741304367E-4 TGTGCCAGCAGTACACCTAGGGGGGGTCCCTATAATTCACCCCTCCACTTT CASSTPRGGPYNSPLHF TRBV6-6 TRBD1 TRBJ1-6 12 18 24 28
638 7.088951901794683E-4 TGCGCCAGCAGCCAAGGGGAAGGATACGAGCAGTACTTC CASSQGEGYEQYF TRBV4-1 . TRBJ2-7 16 -43 -43 24
637 7.077840691917262E-4 TGTGCCAGCAGCTTGGGGAATCAGCCCCAGCATTTT CASSLGNQPQHF TRBV5-5 . TRBJ1-5 16 -46 -46 18
630 7.000062222775313E-4 TGTGCCAGCAGCCAGGACAGTTTGGGTTTTCGGGATGAAAAACTGTTTTTT CASSQDSLGFRDEKLFF TRBV14 . TRBJ1-4 17 -31 -31 34
623 6.922283753633366E-4 TGTGCCAGCAGTTCTACGAGAGACAATGAGCAGTTCTTC CASSSTRDNEQFF TRBV7-6 . TRBJ2-1 11 -43 -43 22
614 6.822282864736575E-4 TGTGCCAGCAGTGAAGCCGAAGGGGGCGGTCAGCCCCAGCATTTT CASSEAEGGGQPQHF TRBV6-1 TRBD1 TRBJ1-5 17 20 28 29
604 6.711170765962365E-4 TGCGCCAGCAGCGACTCCCTCCCCGCCCCCTACAATGAGCAGTTCTTC CASSDSLPAPYNEQFF TRBV5-1 TRBD2 TRBJ2-1 12 16 23 28
604 6.711170765962365E-4 TGTGCCAGCAGCCACCGCTCCGGGACAGGGGCGCCATATGGCTACACCTTC CASSHRSGTGAPYGYTF TRBV3-2 TRBD1 TRBJ1-2 14 19 35 36
589 6.544502617801048E-4 TGCGCCAGCAGCCAAGAGGGCTCATCTGGGGCCAACGTCCTGACTTTC CASSQEGSSGANVLTF TRBV4-3 . TRBJ2-6 17 -34 -34 24
585 6.500057778291362E-4 TGCAGTGCCAGACGAGCGGGGGGCGACTACGAGCAGTACTTC CSARRAGGDYEQYF TRBV20-1 TRBD2 TRBJ2-7 12 14 24 26
570 6.333389630130045E-4 TGTGCCAGCAGTGAACCCGGAGTCTCCTATAATTCACCCCTCCACTTT CASSEPGVSYNSPLHF TRBV6-1 . TRBJ1-6 15 -34 -34 18
554 6.155610272091307E-4 TGTGCCAGCAGCCCCGATTACTATAGCAATCAGCCCCAGCATTTT CASSPDYYSNQPQHF TRBV7-2 . TRBJ1-5 12 -37 -37 15
553 6.144499062213886E-4 TGTGCCAGCAGTTCCGGGATCGGGGCCTACGAGCAGTACTTC CASSSGIGAYEQYF TRBV6-5 TRBD1 TRBJ2-7 13 13 25 25
548 6.088943012826781E-4 TGTGCCAGCAGCCCCGGGGCCACGCAGCTGAACACTGAAGCTTTCTTT CASSPGATQLNTEAFF TRBV3-2 TRBD2 TRBJ1-1 13 13 18 28
533 5.922274864665464E-4 TGTGCCATCGGGACAGGGGACACCAATCAGCCCCAGCATTTT CAIGTGDTNQPQHF TRBV10-3 TRBD1 TRBJ1-5 9 9 19 23
531 5.900052444910622E-4 TGTGCCAGCTCCTGGAGAGCGGGTAGCACAGATACGCAGTATTTT CASSWRAGSTDTQYF TRBV19 TRBD2 TRBJ2-3 8 17 23 23
527 5.855607605400937E-4 TGTGCCAGCAGTTACGGGAGGACTAGGAGATACAATGAGCAGTTCTTC CASSYGRTRRYNEQFF TRBV6-5 TRBD2 TRBJ2-1 15 19 26 30
524 5.822273975768673E-4 TGTGCCAGCAGTGAAACCAGCGGGGGGGCAGATACGCAGTATTTT CASSETSGGADTQYF TRBV6-1 TRBD2 TRBJ2-3 15 15 28 28
521 5.78894034613641E-4 TGTGCCAGCAGTCATATACGGGGCTGCCATCGCAATCAGCCCCAGCATTTT CASSHIRGCHRNQPQHF TRBV28 TRBD1 TRBJ1-5 12 19 24 24
520 5.777829136258989E-4 TGTGCCAGCAGTTACTCGTTGACTAGCGATGAGCAGTACTTC CASSYSLTSDEQYF TRBV6-3 TRBD2 TRBJ2-7 18 20 28 30
518 5.755606716504147E-4 TGTGCCAGCAGCCAGACAGGGGCTAATGAAAAACTGTTTTTT CASSQTGANEKLFF TRBV3-2 TRBD1 TRBJ1-4 14 14 22 22
514 5.711161876994462E-4 CGTGCCAGCAGCTTCCGGGACAATCAGCCCCAGCATTTT RASSFRDNQPQHF TRBV7-4 TRBD2 TRBJ1-5 14 14 20 20
509 5.655605827607356E-4 TGTGCCAGCAGTGAAGTACTGGATAATTCACCCCTCCACTTT CASSEVLDNSPLHF TRBV6-1 . TRBJ1-6 16 -40 -40 22
498 5.533382518955724E-4 TGTGCCAGCAGCTATAGGACAGGGGACTCCTACGAGCAGTACTTC CASSYRTGDSYEQYF TRBV5-5 TRBD1 TRBJ2-7 13 16 23 23
498 5.533382518955724E-4 TGTGCCAGCAGTTACTCTCGATGGGACATGGCTGGCTACACCTTC CASSYSRWDMAGYTF TRBV6-6 TRBD1 TRBJ1-2 17 22 31 32
496 5.511160099200882E-4 TGTGCCAGCAGTTACTCGACTTACGGAAACACCATATATTTT CASSYSTYGNTIYF TRBV6-5 . TRBJ1-3 19 -40 -40 24
496 5.511160099200882E-4 TGTGCCAGCAGCGTAGCCGAGGGACTCGATATCACAGATACGCAGTATTTT CASSVAEGLDITDTQYF TRBV9 TRBD2 TRBJ2-3 17 20 26 29
494 5.488937679446039E-4 TGTGCCAGCAGCCTCAGCGGGGGGGCCCAAAATGAGCAGTTCTTC CASSLSGGAQNEQFF TRBV7-3 TRBD2 TRBJ2-1 12 15 28 30
488 5.422270420181513E-4 TGTGCCAGCAGACGGGGACGGCGGAACACTGAAGCTTTCTTT CASRRGRRNTEAFF TRBV28 TRBD2 TRBJ1-1 11 14 22 23
488 5.422270420181513E-4 TGTGCCGTCCAAACAGGGAGTGGGGAGCTGTTTTTT CAVQTGSGELFF TRBV7-9 TRBD1 TRBJ2-2 6 12 18 21

End of preview. Expand in Data Studio

Benchmark datasets from various AIRR tools and algorithms, including, but not limited to

VDJtools
VDJdb
ALICE
TCRnet
GLIPH/GLIPH2
pyigmap

Note on some external datasets used:

gliph/ data comes from Glanville J, Huang H, Nau A, Hatton O, Wagar LE, Rubelt F, Ji X, Han A, Krams SM, Pettus C, Haas N, Arlehamn CSL, Sette A, Boyd SD, Scriba TJ, Martinez OM, Davis MM. Identifying specificity groups in the T cell receptor repertoire. Nature. 2017 Jul 6;547(7661):94-98. doi:10.1038/nature22976 and Huang H, Wang C, Rubelt F, Scriba TJ, Davis MM. Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening. Nat Biotechnol. 2020 Oct;38(10):1194-1202. doi: 10.1038/s41587-020-0505-4.
alice/mlr data comes from Emerson RO, Mathew JM, Konieczna IM, Robins HS, Leventhal JR. Defining the alloreactive T cell repertoire using high-throughput sequencing of mixed lymphocyte reaction culture. PLoS One. 2014 Nov 3;9(11):e111943. doi: 10.1371/journal.pone.0111943.

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