search

bcgsc / tigmint

⛓ Correct misassemblies using linked AND long reads
https://bcgsc.github.io/tigmint/
GNU General Public License v3.0
54 stars 13 forks source link

Forward+reverse + long reads #115

Closed aabaricalla closed 1 year ago

aabaricalla commented 1 year ago

Hi there! I'm reading the documentation and I have a few doubts.

I have 10X linked reads (forward+reverse) and a Pacbio+ONT longreads files.

What would be the best choice to run first: Tigmint or Tigmint-Long? If tigmint is the choice, I should pre-align each read in a separate round of BWA and then sort+merge them?

Thanks in advance!

lcoombe commented 1 year ago

Hello @aabaricalla,

We haven't done a lot of tests with running sequential Tigmint runs using the different read evidence, but I tend to work with the rule of thumb of using shorter-range evidence first, then longer-range later. So, I'd suggest running Tigmint-long first. Depending on how large your genome is, the other option would be to run your pipeline with both orders of Tigmint, and then see which of them gives you the best result.

For your linked read question - are your linked reads separated into multiple files?

Thanks for your interest in Tigmint! Lauren

aabaricalla commented 1 year ago

Hi @lcoombe, thanks for the quick response. I have a forward + a reverse (10x_Genomics_1.fastq.gz + 10x_Genomics_2.fastq.gz). What's your suggestion in this case? run twice? interleave the files?

lcoombe commented 1 year ago

Hi @aabaricalla, With separate forward/reverse files, the easiest thing to do would be to interleave the forward/reverse files to a single fastq file. Then, you could just use the tigmint-make Makefile to run all the Tigmint steps for you. It's best to run the alignments of the forward/reverse reads together with bwa since it can use pairing information in generating the alignments.

github-actions[bot] commented 1 year ago

This issue has been automatically marked as stale because it has not had any recent activity. It will be closed if no further activity occurs. Thank you for your interest in Tigmint!