Modifying Aligner Parameters for "exome-seq" Preset

[sophiecwebster]

Hello!

I am hoping to run MiXCR on scDNA sequencing targeted to a panel of genes that includes the IG and TR loci (among others). We are sequencing single cells' DNA with the ResolveOME protocol (fragmented shotgun sequencing) and are primarily interested in reconstructing B cell receptor sequences. Thus, I was hoping to run MiXCR on my BAM files with the exome-seq preset and use kAligner2. Does this sound like the best way to work with this data type? If so, I've seen that exome-seq uses kAligner, but I'd like to use kAligner2 because we're expecting our B cells to have high levels of SHM. Is it possible to modify the exome-seq preset to use kAligner2?

Thank you so much!

[mizraelson]

Hi Sophie,
exome-seq is the right preset for that. kAligner is now optimized for both T and B cells. Its only on earlier versions of MiXCR we used two different aligners, but. the one we have now is tuned to identify both.

Sincerely,
Mark

[sophiecwebster]

Thank you so much for the clarification, Mark! El El vie, ago 14, 2026 a la(s) 9:50 p.m., mizraelson < ***@***.***> escribió:

…

Hi Sophie, exome-seq is the right preset for that. kAligner is now optimized for both T and B cells. Its only on earlier versions of MiXCR we used two different aligners, but. the one we have now is tuned to identify both. Sincerely, Mark — Reply to this email directly, view it on GitHub <#2129?email_source=notifications&email_token=ANDIAJGJIXPY67VMB3HEZVT5J53QLA5CNFSNUABIM5UWIORPF5TWS5BNNB2WEL2ENFZWG5LTONUW63SDN5WW2ZLOOQXTCOBQGIZDCMBSUZZGKYLTN5XKMYLVORUG64VFMV3GK3TUVRTG633UMVZF6Y3MNFRWW#discussioncomment-18022102>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANDIAJBQZVI7NRXS2OIEM5L5J53QLAVCNFSNUABHKJSXA33TNF2G64TZHMZTGMJTGQ2TSNZ3IRUXGY3VONZWS33OHMYTANRRGUYTMNNBOYBA> . Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS <https://github.com/notifications/mobile/ios/ANDIAJGXT4OGYDO7UPQH5A35J53QLA5CNFSNUABIM5UWIORPF5TWS5BNNB2WEL2ENFZWG5LTONUW63SDN5WW2ZLOOQXTCOBQGIZDCMBSUZZGKYLTN5XKMYLVORUG64VFMV3GK3TUVJTG633UMVZF62LPOM> and Android <https://github.com/notifications/mobile/android/ANDIAJDFPWW6BDLXA6PDIJT5J53QLA5CNFSNUABIM5UWIORPF5TWS5BNNB2WEL2ENFZWG5LTONUW63SDN5WW2ZLOOQXTCOBQGIZDCMBSUZZGKYLTN5XKMYLVORUG64VFMV3GK3TUVZTG633UMVZF6YLOMRZG62LE>. Download it today! You are receiving this because you authored the thread.Message ID: ***@***.***>