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1. BWA mem to align my genome (ref.fa) to Illumina DNA seq reads
2. Freebayes to get variants
3. VCFtools to filter variants only in the CDS region > cds.vcf
Now I want to use cds.vcf to generate…
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-l, --gene_list path/to/list_of_genes_for_consensi (Consensus sequences are generated for genes in this file. Example provided)
Didn't find the provided example for this file.
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### Ask away!
I am running the wf-amplicon on PCR amplicons covering a complete virus genome (4 overlapping long amplicons per sample, pooled in one barcode) and map the reads to a reference genome o…
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When trying to build racon on a computer with an apple-m1 chip it gives the error "error: unknown target CPU 'apple-m1'
note: valid target CPU values are: nocona, core2, penryn, bonnell, atom, silver…
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I have a naive question about your MSA methodology. Why would the aligner choose to align short segments (1000bp) before aligning again? Perhaps I am misunderstanding the parameters to abPOA.
E…
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I have data that the insert is long enough that it isn't guaranteed to repeat twice within a read but could have partial repeats. I used a previous version of TideHunter that allowed me to set the min…
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Hi
I found this R package quite handy after writing my own custom functions which were otherwise verbose. I have begun to like using this package but I have queries related to `identity` and `cover…
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Hi,
I ran into the panic below while creating a consensus from poa:
`thread '' panicked at 'index out of bounds: the len is 478 but the index is 478', /home/wdecoster/.cargo/registry/src/index.c…
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Hi there,
We want to report an issue with a PanGraph that we generated on a dataset representing 1000 E. coli sequences. We believe that 64 of these sequences are not represented correctly by the P…
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Hi Erik
I've followed your PGGB updates and am now using smoothxg with added consensus paths. I've put the graph into VG and sequenceTubeMap. I notice I have 8 different consensus paths in my graph…