User: samuel.a.odonnell
samuel.a.odonnell • 70
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Posts by samuel.a.odonnell
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C: structural variants from mauve
... One possibility would be to generate multiple genome assemblies (considering it is a single bacterial genome it shouldn't take so long and many are much faster than canu) and see if they all contain the same rearrangements. To check all the genomes for similar rearrangements you could use a tool lik ...
written 6 weeks ago by
samuel.a.odonnell • 70
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C: Building pangenome reference
... You are reaching into the realm of genome graphs, a single space representing multiple genomes
Look into the vg toolkit, cactus alignment and pggb
It will require new whole genome alignments in order to generate the graph (cactus and pggb) which can then be used by vg in order to use the graph in pa ...
written 7 weeks ago by
samuel.a.odonnell • 70
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... You may want to look at using an ensemble approach, employing manta alongside other SV calling tools. Would allow you to be more confident in any call identified by multiple tools ...
written 8 weeks ago by
samuel.a.odonnell • 70
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C: Combining nanopore libraries
... Just to note, I think you were correct to have added the ultra-long reads for genome assembly, it will definitely help with contiguity
Also perhaps you want to try alternative polishing pipeline such as [Racon][1] and [Medaka][2], which are much faster and appear to give similar results
[1]: ht ...
written 8 weeks ago by
samuel.a.odonnell • 70
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... Considering you are looking for contigs I am going to assume that you mean '.fa' and not '.fq' (as stated in the original question).
How do you know which contig you want from each multi-fasta file? Do you have a file with the desired contig and it's corresponding multi-fasta file? ...
written 8 weeks ago by
samuel.a.odonnell • 70
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Comment:
C: Haplotyping Using Whatshap
... - I don't know how feasible this is but can you *de-novo* assemble and then use this genome as the reference for phasing with whatshap?
- when you say you have 5276 genes, how is this data organised?
- what are the gaps that bcftools will fill? ...
written 8 weeks ago by
samuel.a.odonnell • 70
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... Are you asking for SV detection based on whole genome alignment? I.e. your new assembly versus this "close species genome"?
Two tools that consider a range of SV's include [MUM&Co][1] and [syri][2]
You might want to rewrite your question to be more clear
[1]: https://github.com/SAMtoBAM/MUMa ...
written 8 weeks ago by
samuel.a.odonnell • 70
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... I would go with the recommendation in the canu documentation to phase by other means and then reassemble.
I just released [this][1] pipeline to do this using [whatshap][2].
However if you don't have illumina reads, in order to call variants to be phased you might want to use something like [DeepVari ...
written 3 months ago by
samuel.a.odonnell • 70
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... One way is to linearise all the contigs so they are contained within a single line (incase they are not)
`awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' | grep "\S"`
and then use `grep -A1` with the contig name to grab the line with the name and then the contig th ...
written 3 months ago by
samuel.a.odonnell • 70
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... I am not sure if your system to detect homozygous and heterozygous SNPs is common (using a five read threshold) but perhaps you want to try using GATK to call variants instead? ...
written 3 months ago by
samuel.a.odonnell • 70
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