Citing stitchr

The manuscript describing and validating stitchr is available here:

James M Heather, Matthew J Spindler, Marta Herrero Alonso, Yifang Ivana Shui, David G Millar, David S Johnson, Mark Cobbold, Aaron N Hata, Stitchr: stitching coding TCR nucleotide sequences from V/J/CDR3 information, Nucleic Acids Research, 2022, gkac190, https://doi.org/10.1093/nar/gkac190.

The corresponding analyses and related datasets are available here (which used v1.0.0 stitchr scripts).

This citation can be printed in the command line by running stitchr --cite. This command will also output a summary of the underlying data as downloaded from the reference source (particularly the release ID and download date) for every species locally available, which ideally should be reported when publishing sequences produced using stitchr for reproducibility purposes.

Licensing information

stitchr and its related scripts and documentation are provided under an MIT license.

By default, stitchr currently expects IMGT as its reference database, made possible for eligible researchers by separately downloading the reference data IMGT makes publicly available. As stated on their website and in their publications, IMGT’s policy regarding sharing of their data is that:

“… IMGT® software and data are provided to the academic users and NPO’s (Not for Profit Organization(s)) under the CC BY-NC-ND 4.0 license. Any other use of IMGT® material, from the private sector, needs a financial arrangement with CNRS.”

Note that I am not affiliated with IMGT, and am in no way responsible for the content or management of their resources. Please TCR responsibly.