tombo
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nanoporetech
Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.
Dear All, I have some issues with the installation of tombo with bioconda. I read from previous issue posts, that the version of python and the update of conda could...
Hello, I am trying to use the DENA package, which uses Tombo. However, when importing Tombo ("from tombo import tombo_helper, tombo_stats, resquiggle"; not even when using any of its functions)...
Hey, I am trying to install tombo using pip and or the git repository and I get the same error. Below you can find the details: OS: Ubuntu18.04 Python: 3.8...
I am pretty new to Python, so I apologise if this is a very obvious fix. I have tried installing with conda and pip, but neither works for me. With...
Hi all. I'm trying to produce a plot with density curves for a sample and control. When using the following command, the output is the default raw reads plot. Any...
I am not an expert in unix or programming, but am able to follow directions. When I tried to install Tombo after having followed the instructions for the installation of...
Hi， I run resquiggle on my test data ,the command as follows: thread=2 params_fast5=/public211/lirui/m6Adection/data/GCP1/test params_ref=/public211/lirui/m6Adection/data/reference/Arabidopsis_thaliana.TAIR10.cdna.all.fa tombo resquiggle --rna --processes ${thread} --corrected-group RawGenomeCorrected_000 --basecall-group Basecall_1D_000 \ --include-event-stdev --overwrite --ignore-read-locks ${params_fast5} ${params_ref}...
When resquiggling my reads, about 60 % fail with the error *Read event to sequence alignment extends beyond bandwidth*. If I understood correctly this depends on the length of the...
Dear developers, I have used tombo resquiggle without a command `--processes`，the expect process time is 24hours. Then , I used `--processes 40` and `--processes 50` to to run tombo resquiggle...
 I wonder if anyone met the same issue before... Thank you.
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Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.