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snijderlab / stitch

Template-based assembly of proteomics short reads for de novo antibody sequencing and repertoire profiling
MIT License
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How to create templates for a new species #232

Closed biocc closed 1 year ago

biocc commented 1 year ago

Dear Sir,

I am writing to inquire about a specific software mentioned in the user's manual of Stitch. According to the manual, it is stated that the software, assembler.exe, is capable of generating templates for a new species. However, I am uncertain about the exact details of assembler.exe and where I can download it. I was wondering if you could kindly provide me with more information regarding this software. -assembler.exe download "Homo sapiens" -assembler.exe download "Cricetinae gen. sp." "IGHV IGKV,IGLV IGHJ IGLC"

Thank you very much for your attention and assistance. I look forward to your reply.

Best regards, wb J

douweschulte commented 1 year ago

Thank you for opening the issue. The assembler.exe mentioned here is the old name for the stitch.exe this is fixed in newer version of the manual. Since the release of 1.4.0 I reworked the download code quite a bit, and added some additional fixes today thanks to your question, if the release of 1.4.0 breaks when downloading you can try with the nightly version.

Also note that this scrapes the following webpage from IMGT so anything that is not listed there cannot be downloaded by this program.

If you have any other questions feel free to reach out. And if the download does not work out for the species you want to work with, feel free to ask me, I could try the template preparation from my side.