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GuoBioinfoLab / CATT

An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data.
http://bioinfo.life.hust.edu.cn/CATT/
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Question on the running speed #19

Open xuezhang335 opened 6 months ago

xuezhang335 commented 6 months ago

@aqzas @Huffyphenix ， I am using CATT to extract TCR/BCR information from data from scRNA-seq of immune cells, involving more than 100 datasets. Your article gives a performance comparison of each tool, but is there any comparison in terms of task run speed? This will help me a lot, thanks!

aqzas commented 6 months ago

Sorry for the late reply. Regarding the issue of running speed on single cells, a lot has changed since we evaluated it a long time ago. TRUST has been upgraded to v4, MiXCR has also changed its API (seems to be closed source now), and CATT has been rewritten in Julia. Based on our recent usage on single cells, TRUST4 is the fastest, followed by CATT, then MiXCR.

On Fri, Apr 19, 2024 at 4:58 PM Xue Zhang @.***> wrote:

@aqzas https://github.com/aqzas @Huffyphenix https://github.com/Huffyphenix ， I am using CATT to extract TCR/BCR information from data from scRNA-seq of immune cells, involving more than 100 datasets. Your article gives a performance comparison of each tool, but is there any comparison in terms of task run speed? This will help me a lot, thanks!

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