User: colindaven

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colindaven2.6k
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Hannover Medical School
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Staff Scientist Bioinformatics

Posts by colindaven

<prev • 422 results • page 1 of 43 • next >
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Answer: A: Deciding on the best read length for metagenomics
... 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 colindaven2.6k
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Comment: C: ONLINE TRAINING -GENOME ASSEMBLY USING OXFORD NANOPORE SEQUENCING
... 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 colindaven2.6k
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Comment: C: What is the best way to assemble Illumina paired end reads?
... 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 colindaven2.6k
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Answer: A: Programmatically retrieving taxon classification
... Have a look at https://github.com/shenwei356/taxonkit , I think it's exactly what you need ...
written 10 days ago by colindaven2.6k
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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 colindaven2.6k
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Answer: A: how to parse a .fasta file in python ?
... 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 colindaven2.6k
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Comment: C: How to handle multiple contig outputs from de novo assemblers when one contig is
... 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 colindaven2.6k
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Answer: A: Find repeat regions on 100 eukaryotic assemblies
... 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 colindaven2.6k
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Comment: C: Best open source genome browser in 2020
... 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 colindaven2.6k
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Answer: A: Best open source genome browser in 2020
... 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 colindaven2.6k

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Scholar 10 days ago, created an answer that has been accepted. For A: Gene annotation pipeline for bacteria
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Bioinformatics PhD position in Next Generation Sequencing analysis
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Gene annotation pipeline for bacteria
Popular Question 3 months ago, created a question with more than 1,000 views. For Using the MinION MinKNOW software on Ubuntu 1604
Scholar 4 months ago, created an answer that has been accepted. For A: Gene annotation pipeline for bacteria
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Scholar 5 months ago, created an answer that has been accepted. For A: Gene annotation pipeline for bacteria
Scholar 5 months ago, created an answer that has been accepted. For A: Gene annotation pipeline for bacteria
Appreciated 9 months ago, created a post with more than 5 votes. For A: Gene annotation pipeline for bacteria
Scholar 9 months ago, created an answer that has been accepted. For A: Gene annotation pipeline for bacteria
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Popular Question 10 months ago, created a question with more than 1,000 views. For Using the MinION MinKNOW software on Ubuntu 1604
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