Low subsampling fraction

[kwantn]

Hi Nicolas and people,

Thanks to the many posts here I managed to jump over several hurdles to actually complete a NOVOPlasty assembly. I am working with formalin fixed museum samples. I am very keen to try understand what is causing the low Subsampled fraction of 4.92%.

Output in a nutshell:

Attached the log & log_extended:
log_extended_HrtgMZ1_08082024.txt
log_HrtgMZ1_08082024.txt

Key info:

Subsampled reads 4.92%! PE reads uncompressed, 60GB worth for each of 1:N:0 and 2:N:0. Reads id structure seems fine - image inserted below.
WGS of formalin archive samples - so fragmented DNA. See inserted FASTQC report Sequence Length Distribution.
Any questions/thoughts welcomed. Looking forward to hearing from you all.

Cheers
Kwan
FASTQC sequence length distribution

reads ID structure

[ndierckx]

Hi, Sorry I completely overlooked your post so forgot to answer
Probably to late now, but the Subsampled fraction is because it is probaply a very big file and you only have 15 GB of memory, so if you want to use more data, you need to use a HPC.

But I think NOVOPlasty is maybe not the best way to assemble degraded DNA samples, because there will probaply be gaps in coverage and this a problem for NOVOPlasty...

[kwantn]

Hi Nicolas, Thanks for the response and it is never too late. =) I was running it off HPC. I ended up checking the bwa alignment and surely it was very patchy. NOVOPlasty would have disliked that. Cheers Kwan From: Nicolas Dierckxsens ***@***.***> Sent: Thursday, 14 November 2024 12:03 PM To: ndierckx/NOVOPlasty ***@***.***> Cc: Tzu Kwan ***@***.***>; Author ***@***.***> Subject: Re: [ndierckx/NOVOPlasty] Low subsampling fraction (Issue #232) Hi, Sorry I completely overlooked your post so forgot to answer Probably to late now, but the Subsampled fraction is because it is probaply a very big file and you only have 15 GB of memory, so if you want to use more data, you need to use a HPC. But I think NOVOPlasty is maybe not the best way to assemble degraded DNA samples, because there will probaply be gaps in coverage and this a problem for NOVOPlasty... — Reply to this email directly, view it on GitHub<#232 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A37J47ZRWKZDTOLNPIFYOC32APZFZAVCNFSM6AAAAABMVFFGJKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINZVGEZTMMBTGA>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>> This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.