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My problem is that I am having difficulty obtaining a list of variants using bcftools mpileup and bcftools call with PacBio data. I do not have this problem with data of Illumina paired-end sequencing…
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**Deliverable this task is associated with**
_See Deliverables tab here: https://docs.google.com/spreadsheets/d/1z_b6WbuTk4pI0Q-Z-rfCgC-8R3m3F2_JDevYuK8CjYE/edit?usp=sharing_
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**RACI**
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Hi All, first wanted to thank you for developing this tool. I work in a lab that currently focuses on pathogenic species of bacteria that are associated with the microbiome of various tumors and are i…
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I used `fqzcomp -n2 -s4+ -q1` on PacBio HiFi (Sequel II CSS) fastq sequences and recieved (fqzcomp v4.6):
> Quality scale is too high. This looks like Illumina+64 format.
> Try rerunning with the …
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Hello! I have some samples that we have no Illumina reads for. Do you have any sense of whether the PacBio data will produce the split reads to work appropriately in your software?
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### Description of feature
There has been a request for a PacBio only run. This is something not currently supported, however, should be simple enough to implement. Related to #115
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P_filter Minimum Subread Length: 50
P_filter Minimum Polymerase Read Quality: 0.75
N50 Polymerase Read Length after filtering: 2818
N50 Subread Length after filtering: 940
Mean Mapped Subread Conc…
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•Develop your final analysis script and XML files in GitHub, and in a new issue
on github:
• record link to xml file
settings.xml: https://github.com/wangna62691/PacBio_Assembly/blob/master/setting…
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Now that we've reconfigured and refactored the phasing pipeline to improve SV performance on 10Mbp, we probably need to make additional changes to improve scalability for whole chromosome/genome runs.…
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Hi all,
I am new to the field and I'd like to verify my variant calling pipeline using latest CHM13 as reference. I have the HG002v1.1.fasta here and I got the truth set v1.1.vcf from NIST.
> (ht…