DecodeGenetics/Ratatosk

Issues

• Handling highly heterozygous genomes in Ratatosk

  #50 opened 8 months ago by cahuparo
  4

• version 0.9.0 on conda error

  #51 opened 8 months ago by juyanmei
  2

• Use Ratatosk to polish assembly

  #48 opened a year ago by bsb2014
  0

• #Couldn't remove temporary file#

  #41 opened a year ago by Catherine9826
  3

• a question on command line

  #47 opened 2 years ago by shinlin77
  27

• Remove bifrost from code and add it as a requirement

  #45 opened 2 years ago by loraine-gueguen
  2

• /usr/local/bin/Ratatosk Permission denied

  #46 opened 2 years ago by kangxiongbin
  2

• Conda installation

  #27 opened 2 years ago by rivera10
  4

• Can I reuse the existing indexes in correction of another long reads?

  #43 opened 2 years ago by asan-emirsaleh
  2

• UMI reads

  #20 opened 4 years ago by kokyriakidis
  3

• Reference-guided SLURM script errors

  #22 opened 4 years ago by ASLeonard
  6

• Sharding the second correction pass?

  #23 opened 4 years ago by ASLeonard
  3

• short reads for correction

  #24 opened 4 years ago by PetrNguyen
  1

• Correction Nanopore reads using PacBio HiFi reads?

  #29 opened 3 years ago by jflot
  1

• -i or -s?

  #37 opened 3 years ago by hbeale
  1

• Can I split stage 1 indexing onto subsequent jobs?

  #40 opened 2 years ago by asan-emirsaleh
  7

• questions re index construction & insert size

  #42 opened 2 years ago by rwhetten
  2

• Can you run "correct -2" phase without "correct -1"?

  #39 opened 2 years ago by tolarnik
  2

• Index generation

  #38 opened 3 years ago by Akazhiel
  8

• Reference-guided Ratatosk on Single Node with chromosomes but many unplaced scaffolds - faster with GNU Parallel?

  #25 opened 4 years ago by jelber2
  2

• non-{A,C,G,T} characters appearing in the corrected reads

  #26 opened 4 years ago by ASLeonard
  5

• Installation typo & Docker

  #30 opened 3 years ago by hoelzer
  2

• Input file format

  #31 opened 3 years ago by OZTaekOppa
  1

• Treated as HiFi or PacBio Raw

  #32 opened 3 years ago by OZTaekOppa
  1

• how to create a single short read file

  #33 opened 3 years ago by gunjanpandey
  5

• Installation issue

  #34 opened 3 years ago by gettl008
  7

• Run time estimation

  #35 opened 3 years ago by Akazhiel
  15

• Ratatosk::correct(): Corrected read file is not in the same order as input long read file. Abort.

  #36 opened 3 years ago by kgun12
  2

• checkpointing / breaking up job

  #17 opened 3 years ago by jo-mc
  4

• Fastq input format for short reads

  #28 opened 4 years ago by jianshu93
  2

• Feature request: Reference guided correction - locally

  #14 opened 4 years ago by rahulvrane
  8

• Advice and request on genome-guided polishing with BAM files

  #19 opened 4 years ago by andreaswallberg
  1

• Corrected PromethION reads are extremely short

  #18 opened 4 years ago by andreaswallberg
  11

• cant get a fastq output

  #21 opened 4 years ago by HadrienRegue
  2

• Excessive memory usage on a small diploid genome

  #15 opened 4 years ago by mikolmogorov
  7

• Ratatosk in de novo or reference mode

  #16 opened 4 years ago by jelber2
  4

• Wrong parameter -i

  #13 opened 4 years ago by flystar233
  1

• adjustable kmer size

  #12 opened 4 years ago by HenrivdGeest
  17

• Found 0 unique k-mers

  #9 opened 4 years ago by sbultmann
  7

• Corrected reads as good as Hifi reads?

  #11 opened 4 years ago by dabitz
  4

• Is it possible to add option to split uncorrected regions instead of "trimming" them?

  #6 opened 4 years ago by jelber2
  12

• Resume from the last completed stage

  #10 opened 4 years ago by lyrk50
  1

• Is it good to run Ratatosk on multiple long read files separately?

  #8 opened 4 years ago by lileiting
  2

• Understanding the -u option (different individuals than -s possible?)

  #7 opened 4 years ago by jelber2
  2

• Docker

  #5 opened 4 years ago by husamia
  2

• Add explicit sequence anchoring subcommand

  #3 opened 4 years ago by phiweger
  6

• Make fails in MacOS Catalina

  #4 opened 4 years ago by bstamps
  2

• compiling - pthreads and usage of -s parameter

  #1 opened 4 years ago by colindaven
  5