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inmorispi/HG-CoLoR (press backspace or delete to remove)

Hello, I m running HgColor (installed from the github repo) to correct Nanopore reads (~30x) using Illumina reads (~150x): /home/bin/HG_CoLoR/HG_CoLoR --longreads ONT_filtered.fasta --shortreads short.fastq ...
  • JuliaLopezDelgado
  • 2
  • Opened 
    on Jan 19, 2021
  • #19

Hey @morispi, I am trying to use HG-Color (thank you for the tool) to correct a 5 mbp stretch of ONT reads from the chromosome 1 of HG002. It s about 15K reads with an N50 around 50 kbp. I ran the tool ...
  • GuillaumeHolley
  • 4
  • Opened 
    on Sep 29, 2020
  • #18

Hello. I am trying to run the following code in a SGE script: HG-CoLoR --longreads $long_reads --shortreads $short_reads --tmpdir ./tmp --out HGCcor_long_reads.fasta --nproc 48 I get the following error, ...
  • JuliaLopezDelgado
  • 2
  • Opened 
    on Apr 29, 2020
  • #17

$ install.sh $ In file included from src/seedsLinking.cpp:1:0: src/seedsLinking.h:5:27: fatal error: test/testdata.h: No such file or directory #include test/testdata.h ^ compilation terminated. Why? ...
  • Yunxia-li
  • 1
  • Opened 
    on Nov 20, 2019
  • #16

I am trying to run HG-CoLoR for error correction of PacBio reads with 10x Linked-Reads (short reads). I installed QuorUM with bioconda. I got this error when running HG-CoLoR: ----- QuorUM ----- perl: ...
  • mborche2
  • 5
  • Opened 
    on Nov 18, 2019
  • #15

Which output file should be used for subsequent sequencing? The program only gave me output files in the temporary directory.
  • drs357
  • 2
  • Opened 
    on May 18, 2019
  • #14

Hello, I m trying to use HG-CoLoR to correct minion reads with illumina reads but i end up with a error at the Blasr step : [INFO] 2019-04-30T10:47:00 [blasr] started. Warning: resetting nCandidates ...
  • Seajull
  • 4
  • Opened 
    on Apr 30, 2019
  • #13

Hi, I have some difficulties to run HG-CoLoR, it stops after few seconds. Here is my command (I have about ~100x for short reads) : HG-CoLoR --longreads $LRFASTA --shortreads $SHORTREAD --out $CORRREADS ...
  • MargauxAlison
  • 2
  • Opened 
    on Feb 13, 2019
  • #11

Hi, I am running HG-CoLoR on a local machine, and now it is running since about a week: is that normal? HG-CoLoR --bestn 15 --kmcmem 90 --nproc 18 --longreads ../ONT_181026.fa --shortreads PE4702_200bp_interlaced.fq ...
  • dcopetti
  • 3
  • Opened 
    on Dec 27, 2018
  • #10

Hello, I am about to run HG-CoLoR, but first I wonder if there is a preferred format/coverage of the Illumina data. I have a PE 470 bp library (2x260 bp) and a PE 700 bp (2x150). I am going to correct ...
  • dcopetti
  • 2
  • Opened 
    on Dec 20, 2018
  • #9
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