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We try to polish a rather fragmented genome assembly with racon. So far we are testing thing on Yeast S288C, so we have a decent reference to check for performance. We use very low coverage nanopore r…
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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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Hi there,
I've got a few bacterial assemblies in which I determined some plasmid sequences. I therefore wanted to try out Unicycler to figure out whether it would be able to optimize my Illumina-on…
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Hi
I've recently come across a forum (https://www.biostars.org/p/89088/) which mentions that bwa mem should be run with Phred+33 Illumina reads instead of Phred+64. My Illumina library is Phred+64, a…
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The original Illumina FastQ format used /1 and /2 to indicate paired reads. Starting around 6-12 months ago with the introduction of casava 1.8, the pair identifiers changed so they are separated from…
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It looks like FASTP is not able to detect *automatically* the adapter at all for miRNA-seq data.
For example, FASTP is not able to detect *automatically* the adapter in the SE FASTQ file from https…
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Hello,
I am preparing the short read data with these two scripts, and I wonder if you have some guidelines to help the choice.
I am assembling a 5 Gb genome, I have about 30x cov of 1x260 bp reads…
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The first query works:
```
`$ q -H -d"," "SELECT * FROM JGI_strains.csv WHERE Platform='Illumina'"
1,Hernandeziana,sp.,ATA11-4-KO1,Illumina
2,Aetokthonos,hydrillicola,B3-Florida,Il…
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I get an error like the following:
WARNING: Must specify a merged illumina fastq file with -illumina_1
WARNING: Must specify a merged illumina fastq file with -illumina_2
WARNING: Long read fil…
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Dear Dengfeng,
Thanks for your tool.
I tried to use purge_dups to clean our assembly. I have some questions:
1. we have Pacbio sequencing data and Illumina sequencing data, I want to use all of …