Plant-Food-Research-Open/assemblyqc

Issues

• What organisms is this designed for?

  #124 opened 4 months ago by tseemann
  1

• Reduce report load time

  #142 opened 3 months ago by GallVp
  0

• DNADIFF is killed by out of memory signal on SLURM

  #141 opened 3 months ago by GallVp
  0

• GFF3 validation fails for circular sequences

  #129 opened 3 months ago by GallVp
  2

• Fix flowchart syntax

  #132 opened 3 months ago by GallVp
  1

• `hic` parameter does not allow `.merged.fq.gz` name patten

  #130 opened 3 months ago by GallVp
  2

• Remove Bioconda `defaults` channel

  #135 opened 3 months ago by GallVp
  1

• Add compleasm

  #127 opened 3 months ago by christinawu2008
  1

• Add HiC heatmap for combined haps

  #128 opened 3 months ago by christinawu2008
  0

• Add gfastats

  #126 opened 3 months ago by GallVp
  2

• Gene score distribution graph does not appear correctly

  #125 opened 4 months ago by GallVp
  0

• LAI is not computed for soft mask assemblies

  #117 opened 5 months ago by GallVp
  0

• LTRRETRIEVER_LTRRETRIEVER fails when the input assembly is not writable

  #98 opened 5 months ago by GallVp
  0

• LTR Retriever crashes when input assembly does not contain LTRs

  #92 opened 5 months ago by GallVp
  1

• PLOTSR failure due to `tokenize('.on.')`

  #102 opened 5 months ago by GallVp
  0

• Incorrect CDS Length Distribution Graph

  #95 opened 5 months ago by GallVp
  0

• [UPDATE] GITHUB/SCHNEEBERGERLAB/SYRI -> 1.7.0

  #104 opened 5 months ago by GallVp
  0

• Update NCBI FCS GX

  #93 opened 5 months ago by GallVp
  0

• Mim. Sys Requirements

  #91 opened 5 months ago by GallVp
  0

• Create a summary presence/absence table for NCBI FCS modules

  #88 opened 5 months ago by GallVp
  0

• Can we automatically label sequences for PLOTSR?

  #116 opened 5 months ago by GallVp
  1

• [UPDATE] GITHUB/NCBI/FCS -> 0.5.4

  #114 opened 5 months ago by GallVp
  1

• Update NCBI FCS Adaptor

  #94 opened 5 months ago by GallVp
  1

• [UPDATE] GITHUB/PYTHON/CPYTHON -> 3.12.4

  #113 opened 5 months ago by GallVp
  0

• [UPDATE] GITHUB/OUSHUJUN/EDTA -> 2.2.0

  #112 opened 5 months ago by GallVp
  0

• [UPDATE] GITHUB/SHENWEI356/SEQKIT -> 2.8.2

  #109 opened 5 months ago by GallVp
  0

• [UPDATE] GITHUB/NCBI/SRA-TOOLS -> 3.1.1

  #108 opened 5 months ago by GallVp
  0

• Update docs for `monoploid_ids`

  #86 opened 7 months ago by GallVp
  1

• https://github.com/schneebergerlab/plotsr

  #77 opened 7 months ago by GallVp
  6

• Merqury

  #85 opened 7 months ago by GallVp
  0

• Sort fasta ids in natural order for the HiC module so that the annotations on the HiC map is also in natural order

  #76 opened 7 months ago by GallVp
  0

• NCBI_FCS_GX does not resume always

  #80 opened 7 months ago by GallVp
  0

• Inversions in Synteny

  #82 opened 7 months ago by GallVp
  0

• Create a line plot for synteny

  #74 opened 7 months ago by GallVp
  1

• Further Assessment of Genome Annotation

  #75 opened 7 months ago by GallVp
  2

• Update the LICENSE text

  #81 opened 7 months ago by GallVp
  0

• FASTA_LTRRETRIEVER_LAI failure

  #83 opened 7 months ago by GallVp
  0

• BlobTools

  #90 opened 7 months ago by GallVp
  0

• Patch 1.3.2

  #87 opened 7 months ago by GallVp
  1

• NGenomeSyn

  #84 opened 7 months ago by GallVp
  1

• NCBI FCS GX KRONA plot should be updated to show the div listed in the result column

  #72 opened 8 months ago by GallVp
  0

• Move to BWA-MEM2 for improved performance

  #66 opened 8 months ago by GallVp
  1

• Pass the EDTA gff3 file through genome tools gt gff3 for format correction before saving

  #67 opened 10 months ago by GallVp
  0

• Update Information on Telomere Motifs

  #73 opened 10 months ago by GallVp
  0

• Add information note regarding sequence relabelling file under CIRCOS

  #78 opened 10 months ago by GallVp
  0

• EDTA outputs

  #65 opened a year ago by jtahir
  1

• Fix the test_full example config and docs to exclude the mitochondrion genome from synteny and LAI modules

  #68 opened a year ago by GallVp
  1

• Fix typo in `assamblathon_stats` in nextflow.config

  #69 opened a year ago by GallVp
  1

• Add magnitudes to Krona plots for length based abundance estimates

  #70 opened a year ago by GallVp
  1

• Update readme to include references for new software for LAI and GX subworkflows...

  #71 opened a year ago by GallVp
  1