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I am using bar codes paired end reads where there is a 6 bp bar code on read 1 and a 2 bp bar code on read 2, making these into one tag adding as a comment to both reads before aligning, causes BWA me…
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### Description of feature
Hi,
Illumina has introduced a new read compression format, ORA: https://www.illumina.com/science/genomics-research/articles/design-ora-lossless-genomic-compression.htm…
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I understand that bwa-meth aligns to the c2t converted reference. Would it be possible to change bwa-meth also to align to the g2a converted reference?
I believe this is what bismark calls "--pbat" o…
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Hello,
I am running Scaff10x V.4.2 with the following command:
scaff10x -nodes 40 -longread 1 -plot 10x_coverage.png PacBioScaffolds.fasta 19-Bp_S1_L001_R1_001.fastq.gz 19-Bp_S1_L001_R2_001.fastq.gz…
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Hi there,
I have a strange error while running operams. I launched the tool against an already computed assembly.
`OPERA-MS --short-read1 FastqIllumina/all.bbdukTrimQ15.SludgeDK_1.fastq.gz --sho…
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FYI, the samtools view is not needed since version 1.3 (or earlier possibly)
```
java -jar build/libs/bazam.jar -bam my.bam | \
bwa mem -p ref.fa - | \
samtools view -bSu - | \
…
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Hi,
I have noticed some issues when trying to run your software. It seems that you rely on using the old version of bwa (pre. 0.7) to run the pipeline and for creating the bam input for the system. T…
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Hi Platinum Devs,
I am interested in running the HMFtools pipeline on GCP, but I already have my files aligned with bwa-mem. Is there support for starting with aligned BAMs using Platinum/could you…
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When using coverM, I met the following problem. May I know how to solve it? Thank you.
2022-08-02T06:51:55Z INFO coverm::mapping_index_maintenance] Generating BWA_MEM index for /tmp/.tmpzfBZeD ..
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I've encountered an issue with reproducibility of bwa-mem2 that is likely due to a multi-threading bug. This may be related to the following issue: https://github.com/bwa-mem2/bwa-mem2/issues/215.
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