User: colindaven
colindaven • 2.6k
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Staff Scientist Bioinformatics
Posts by colindaven
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... It sounds like you want to do assembly after sequencing. In that case, always, always, always go for the longest read lengths you possibly can. It's not really a surprise than ONT and Pacbio HiFi and completely dominating the assembly realm, in metagenomics as well.
- SE and PE 75bp are not great, ...
written 4 days ago by
colindaven • 2.6k
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... I am not a fan of the SHOUTING here, please don't do this, even if you are excited about making a lot of money off your workshops. ...
written 8 days ago by
colindaven • 2.6k
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... Maybe you should share more first, or show evidence of effort ? I second Spades, why don't you just try it ? ...
written 9 days ago by
colindaven • 2.6k
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... Have a look at https://github.com/shenwei356/taxonkit , I think it's exactly what you need
...
written 10 days ago by
colindaven • 2.6k
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Answer:
A: filtering alignned seqeunces
... A more standard way to do this would be
1. convert SAM to BAM with BAI index
2. run samtools idxstats x.bam
3. alternative: run samtools stats x.bam
This would give you the stats including number of reads aligned to each reference as a text file. Very useful if you have many references. ...
written 16 days ago by
colindaven • 2.6k
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... Try biopython, from memory they use delimiters such as space to differentiate the ID from the name or annotation fields. It might be helpful to use sed etc in Linux to modify the fasta headers to get the ID and Name to "stick together", depending on what you want to do.
You are right though, fasta ...
written 19 days ago by
colindaven • 2.6k
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... If you have related genomes, potentially ref based scaffolding tools like this are useful.
https://github.com/malonge/RaGOO
https://github.com/combogenomics/medusa ...
written 5 weeks ago by
colindaven • 2.6k
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... You can have a look at MAKER for annotation.
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-491
The DFAM database might help for data, but I don't know if that covers your insects.
https://dfam.org/
Perhaps for large scale projects like this you need to apply for comput ...
written 5 weeks ago by
colindaven • 2.6k
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... I use the server version exclusively. It's not too hard to set up and you want your software where the data lives to avoid endless unnecessary data transfers. ...
written 6 weeks ago by
colindaven • 2.6k
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... I'm a big fan of JBrowse. I prefer it to the likes of IGB and IGV because of the much faster loading times for big BAMs. It also allows you to structure information for users so they can explore data integration.
I haven't tried JBrowse2 yet, but its on my list and brand new in 2020. ...
written 6 weeks ago by
colindaven • 2.6k
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