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Hi,
I installed pacbio_qc with pip install and ran below two commands
` sequana_pacbio_qc --input-directory /data/shared/clinical/LongRead/Data/`
input dir where i have one of BAM file GIAB Tri…
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Thank you for developing this awesome tool.
I was wondering if singlem (specifically the microbial fraction module) would work adequately on Nanopore/PacBio long-read datasets (metagenomic reads an…
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Hi! I'm running long_read_typing.py for PacBio -reads for which I have extracted the HLA-regions (originally aligned data to chm13, then extracted hla with HLA*LA and ran bam2fastq). I was wondering a…
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May I ask if FINDER is compatible with long read sequencing? If not, how do you recommend enhancing the annotation results with the FINDER output using such data?
Thanks a lot!
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Do you know if the bam output is compatible with the pacbio arrow tool which is a bit picky about the format.
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Hi
PacBio data is saved in BAM format and not in FastQ.
Is BAM supported and if not could it please be considered.
Converting 100's of GB BAM files to FastQ takes time and space and running directl…
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Hi,
I am new to Long reads seq and Deepvariant i tried to to WGS Variant calling steps from Alignment ( pbmm2 ) from GIAB data and Variant Call through Deepvariant Singularity Image ( singularity p…
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First, love this tool.
Wondering if the error models for PacBio and Nanopore will be a including in a future release?
Or how would you recommend to include it?
Many thanks,
Rick
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Are you intending to release a PacBio CLR correction model?
If not, have you a procedure we could use to do it?
Cheers,
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