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Old 08-06-2013, 08:10 AM   #1
mikesh
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Post MiTCR: A novel software tool for analysis of T-cell receptor sequencing data

Dear fellow Bioinformaticians,

Allow me to introduce a recently published software tool [Nat. Methods] that allows extremely fast and accurate processing of T-cell receptor repertoire high-throughput sequencing data.

Main features include:

1. Extraction of complementarity determining region 3 (CDR3) sequence
2. Determination of variable (V), joining (J) and diversity (D) alleles according to IMGT nomenclature
3. Providing data on insertions and deletions produced by V(D)J recombination
4. Error correction algorithm that eliminates the majority of spurious clonotypes generated by PCR and NGS errors
5. Low system requirements, runs fast on a commodity hardware
6. Well-documented open-source software written in Java

For more information please visit http://mitcr.milaboratory.com

Last edited by mikesh; 08-06-2013 at 01:21 PM.
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Old 04-10-2014, 07:13 AM   #2
F_KVH
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Hi,
Does any one know any new algorithms or software for T-cell receptor except the MiTCR?
Thanks
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Old 04-10-2014, 09:32 AM   #3
mikesh
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Well to the best of my knowledge there are currently no tools able to efficiently process huge amounts of TCR repertoire sequencing data.
If you simply need to do this for several sequences semi-manually, you can use IgBlast http://www.ncbi.nlm.nih.gov/igblast/...LINK_LOC=igtab.
But why are you asking that? If there are some additional features you need, you have some problems running MiTCR or you are not satisfied with MiTCR output, please let us know. We would greatly appreciate any feedback.
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Old 04-10-2014, 09:51 AM   #4
RDW
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One problem is that the website seems to be broken.
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Old 04-10-2014, 10:35 AM   #5
mikesh
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I see We're having some maintenance issues, it will be running soon. I'll post here when it will be up
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Old 04-10-2014, 12:53 PM   #6
mikesh
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MiTCR web page is up and running
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Old 04-10-2014, 02:43 PM   #7
RDW
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Thanks for the quick response!

Is TRgamma/delta now supported?- I see a patch for this was mentioned on Biostars a few months ago.
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Old 04-11-2014, 03:24 AM   #8
mikesh
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Dear all!

Here is a link to binary distribution of MiTCR with support of gamma-delta genes:
http://files.milaboratory.com/mitcr/...beta/mitcr.jar

As we didn’t release it yet, the only option to use it is using plain jar execution. Here is example command:
Code:
java -jar /path/to/mitcr.jar -pset flex -gene TRG input.fastq.gz output.txt
or
Code:
java -jar /path/to/mitcr.jar -pset jprimer -gene TRG input.fastq.gz output.txt
if you are using multiplex primers for the J region that are close to conserved PHE.

The “cls" output for TRG/TRD genes is not supported.

We will update the release package at MiTCR web page with TRG/TRD module in near future
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analysis, ngs, software, t-cell repertoire, tcr

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