KolmogorovLab/hapdup

Issues

• noob questions dual vs phased assembly

  #45 opened 2 months ago by JWDebler
  1

• Phase block and hapdup_phased_{1,2}.fasta

  #43 opened 3 months ago by WeichenZhou
  3

• configure: error: cannot find required auxiliary files: config.guess config.sub

  #44 opened 2 months ago by jflot
  1

• Too good to be true? understanding hapdup results

  #42 opened 6 months ago by cahuparo
  5

• Issue with Hapdup

  #39 opened 6 months ago by santoshe1
  1

• Issue with selection of PEPPER model for new ONT chemistry

  #35 opened 6 months ago by thainsCEB
  5

• ERROR: NO COMMON CONTIGS FOUND BETWEEN THE BAM FILE AND THE FASTA FILE

  #41 opened 7 months ago by Axze-rgb
  6

• ERROR: NO COMMON CONTIGS FOUND BETWEEN THE BAM FILE AND THE FASTA FILE

  #18 opened 2 years ago by bo8883
  4

• Are Dorado reads supported?

  #40 opened 7 months ago by Axze-rgb
  2

• Contigs without assigned phaseblocks in their name

  #38 opened 10 months ago by sivico26
  3

• stderr throw away (2>/dev/null) during polishing steps results in troubleshooting difficulties

  #37 opened 10 months ago by Sam-Koehler
  1

• hapdup_phased_{1,2}.fasta

  #36 opened a year ago by EDISON2022W
  1

• Hapdup did not generate expected folder/files

  #31 opened a year ago by EDISON2022W
  2

• Question about no result from Margin

  #27 opened a year ago by yzhang-github-pub
  7

• Exception: Missing output

  #34 opened a year ago by Andreas-Bio
  2

• Docker installation problem

  #16 opened 2 years ago by rpzhao
  2

• Cannot Find HapDup in Conda

  #33 opened a year ago by FrostFlow13
  1

• Support for CLR reads?

  #32 opened a year ago by ptrebert
  4

• Error to run hapdup-0.12

  #30 opened a year ago by EDISON2022W
  1

• Problem running HapDup

  #29 opened a year ago by mwjraats
  1

• hapdup tool related error

  #28 opened a year ago by dasn588
  4

• --overwrite fails

  #21 opened a year ago by mattloose
  2

• unexpected keyword argument 'index_filename'

  #26 opened a year ago by rmormando
  2

• Flye polisher fails on a bam with `--eqx`

  #24 opened 2 years ago by mikolmogorov
  3

• hapdup fails with multiple primary alignments

  #25 opened 2 years ago by mattloose
  4

• read length inference bug

  #23 opened 2 years ago by WenyuLiang
  1

• Option to set minimap2 -I flag

  #13 opened 2 years ago by fellen31
  3

• compiling errors

  #22 opened 2 years ago by rmormando
  1

• ZeroDivisionError

  #20 opened 2 years ago by mattloose
  4

• Subprocess flye --polish-target fails

  #19 opened 2 years ago by elcortegano
  2

• phase block number compared to Whatshap

  #17 opened 2 years ago by MichelMoser
  3

• Super cool tool! Maybe in the README mention that FASTQ files are required if using the container

  #15 opened 2 years ago by jelber2
  3

• Incorrect genotype for large deletion

  #14 opened 2 years ago by GuillaumeHolley
  7

• A few questions

  #12 opened 2 years ago by GuillaumeHolley
  2

• Some questions about using HapDup

  #11 opened 3 years ago by zmz1988
  2

• invalid contig

  #7 opened 3 years ago by tongyin121
  7

• pthread_setaffinity_np failed Error while running pepper

  #10 opened 3 years ago by LYC-vio
  11

• Docker fails to mount HD_DIR

  #3 opened 3 years ago by alkminion1
  8

• Please add CLI option to specify location of BAM index

  #8 opened 3 years ago by bkmartinjr
  3

• Using Pepper-MARGIN r0.7?

  #9 opened 3 years ago by GuillaumeHolley
  3

• Unable to assemble to chromosomes

  #6 opened 3 years ago by tongyin121
  2

• Changing `pepper_variant` variant calling mode from ONT to HiFi

  #5 opened 3 years ago by aseetharam
  2

• non haploid assembly as input

  #2 opened 3 years ago by kallekarlhugo
  1

• GPU support

  #4 opened 3 years ago by MichelMoser
  2

• Singularity

  #1 opened 3 years ago by GuillaumeHolley
  3