aureliendejode

Quality scores encoding

2

Hello, I am cleaning some Illumina data, some of them are pretty old, and I get quality of 70 in fastp report. When I analyze the same file with fastqc,...

Hello, I plan to use masurca for an hybrid assembly combining PacBo CLR reads and Illumina reads. I read in the documentation that Illumina reads should not be pre-processed. I'd...

Short reads pre-processing before polishing

3

**Question or Expected behavior** I have a reference genome obtained after CANU assembly, purge_dups and long reads polishing with arrow. I'd like to polish with short reads using Next_polish. Should...

Using gff file with merfin ?

3

Hello, I polished my assembly using arrow and I have a .gff file, but no .vcf. Is it possible to run Merfin using a .gff file ? Otherwise do you...

Not finding the mito in assembled CLR data

3

Hello, I tried to find the mitochondrial sequences in my assembly. I assembled CLR PacBio reads using CANU for a mollusc genome. As reference I used 2 mitochondrial genomes of...

Running mitohifi using singularity

2

Hello, My cluster does not have docker but has singularity, so I am trying to use the singularity cmd: singularity exec --bind /path/to/container_directory:/path/to/container_directory docker://ghcr.io/marcelauliano/mitohifi:master mitohifi.py -h I am not familiar...

Dentist parameters

3

Hi, I managed to run the pipeline but know I am having a closer look at the options. My goal is to be conservative with this: I ma happy to...

Using meryl to prepare for Merqury

2

Hi, I'd like to evaluate my assembly. I have several Illumina fastq files. For each library I have one fastq file for Forward and one for Reverse reads. What is...

Hello and thanks for putting together mitoHifi! I just assembled 3 mt genomes from sea anemones and I would like to discuss the quality assessment of those. I have watch...

--busco_lineage helps with busco scores but not with protein number

4

Hello, I have used BRAKER3 with default parameters to annotate 3 anemone genomes and my busco scores were lower than in my genome and so I ran it again using...