ericgonzalezs

HiFIasm is taking to much RAM to run with low coverage data

10

Hi, I am trying to assembly some low coverage HIFI reads for a plant genome. I am running this assembly in a cluster with SLURM. It is easier for me...

Hi, I am not interested in the @SQ lines. I am just wondering if you could please tell me if I can trust the alignments generated with minimap2 if I...

ERROR-purge

1

I am using HIFIASM like this: hifiasm -o Outfile -t 37 --h1 File_Hi-C_R1.fastq.gz --h2 File_Hi-C_R2.fastq.gz Sequel.file.001.ccs.fastq.gz Sequel.file.002.ccs.fastq.gz Sequel.file.003.ccs.fastq.gz I am having the error: "ERROR-purge" Do you know what could be...

3d-dna pipeline to scaffolding a hifiasm heterozygous assembly

3

Hi, I have a haplotype resolved assembly done with hifiasm (HI-C) and Hifi data for a plant genome. I would like to use the 3d-DNA pipeline for the scaffolding and...

Hi, I am running hifiasm 0.19.5-r592 like this: hifiasm -o Outfile -t 37 1.ccs.fastq.gz 2.ccs.fastq.gz I don't have Hi-C data or parental information. The end of the run looks like...

I would like to add x numer of N between concatenated sequences with collapse

2

I would like to concatenate sequences and add a determined number of N between sequences Let's say I have these sequences >seq1 AACC >seq2 CCAA >seq3 CCCT How I could...

error in the file *.combine.scn

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Hello, I am running LTR_FINDER_parallel like this: LTR_FINDER_parallel -seq ARG.fa -threads 10 -harvest_out -size 1000000 -time 300 However the file ARG.fa.finder.combine.scn only contains the header. #LTR_FINDER_parallel -seq ARG.fa -size 1000000...

Hi, snpflip is giving me one position before the position of my original file. example snp flip positions 1 10 1 15 1 25 real positions 1 11 1 16...

Question about diagMum()

1

I am using your code from here: https://jmonlong.github.io/Hippocamplus/2017/09/19/mummerplots-with-ggplot2/ After using your function diagMum() the values of qs and qe are changing For example, by writing only the first 6 columns,...

Can I skip the step that incorporate the coverage biases in HSats?

1

Hi, I would like to run this pipeline in a plant genome. I would like to skip the step4 "incorporation coverage biases in HSats". How I could achieve this if...