leylabmpi/Struo2

Issues

• missing species in GTDB 207 gte50comp-lt5cont.nwk tree

  #49 opened 3 months ago by chloelulu
  2

• Kraken2_build step stalling

  #27 opened 2 years ago by dgolden96
  7

• Pangenomes with Struo2

  #48 opened a year ago by sarpiens
  2

• kraken2-build error when creating sequence ID to taxonomy ID map

  #18 opened 3 years ago by joshsimcock
  9

• Combining fungi and viruses with GTDB

  #11 opened 3 years ago by luhugerth
  6

• How can I use custom genomes and GFF files for HUMAnN database?

  #47 opened a year ago by jolespin
  1

• Using Humann3 files for MetaPhlan?

  #46 opened a year ago by vinisalazar
  2

• Generating sample table when updating database with MAGs - GTDB taxID and Accession Number

  #40 opened 2 years ago by PeterCx
  5

• Feature request - database_download.py should check if the files have already been downloaded successfully

  #45 opened 2 years ago by flashton2003
  2

• GTDB 207 Kraken db vs maxikraken2_1903_140GB db classification rate

  #44 opened 2 years ago by ohickl
  1

• Updating Database: Error with kraken2_add_taxID

  #43 opened 2 years ago by PeterCx
  4

• Error updating Kraken2 GTDB Database with MAGs - MissingOutputException in rule kraken2_cp_to_tmp in file

  #42 opened 2 years ago by PeterCx
  1

• GTDB to NCBI?

  #41 opened 2 years ago by stefanielager
  3

• GTDB Database Download: RecursionError: maximum recursion depth exceeded while pickling an object

  #39 opened 2 years ago by PeterCx
  4

• 0 Bracken added reads with GTDB database for all taxonomic units

  #38 opened 2 years ago by alimayy
  4

• GTDB207 genes_db.tar.gz missing

  #36 opened 2 years ago by SmalJonni
  2

• protein kraken2 DB?

  #35 opened 2 years ago by wwood
  2

• Faster downloads

  #34 opened 2 years ago by wwood
  3

• GTDB202 tree is missing species

  #33 opened 2 years ago by SJohnsonMayo
  3

• amino acid database for HUMAnN3 run

  #32 opened 2 years ago by kk1120
  4

• More detail on classification % and taxonomy issue for Kraken2

  #31 opened 2 years ago by dgolden96
  8

• Kraken2 classification % goes down after adding more genomes

  #29 opened 2 years ago by dgolden96
  4

• GTDB_release207 has empty 150/200/250 Bracken files

  #30 opened 2 years ago by zoey-rw
  4

• A question on time and memory requirement of a helper script "database_download.py"

  #16 opened 3 years ago by ilnamkang
  13

• What is the meaning of D1, D2, D3, C1, C2, C3 etc in Kraken Report

  #28 opened 2 years ago by Rohit-Satyam
  1

• Merging Two or more Kraken Indexes to create most updated Indexes

  #25 opened 2 years ago by Rohit-Satyam
  1

• kraken2 database update function

  #26 opened 2 years ago by dgolden96
  2

• "package humann-3.0.0 is excluded by strict repo priority"

  #24 opened 2 years ago by emaxortiz
  2

• Missing FASTA file paths from bac120 and ar122 GTDB metadata

  #23 opened 2 years ago by dgolden96
  1

• Troubleshooting snakemake_sge.sh

  #22 opened 2 years ago by dgolden96
  8

• Improper visualisation of Kraken2 output after using Struo2 Kraken database files

  #21 opened 2 years ago by Rohit-Satyam
  4

• need gene_db example for update HUMAnN3 with new gene set input

  #19 opened 3 years ago by yiqijiang17
  3

• Cyclic dependency on rule copy_gene_info

  #20 opened 3 years ago by yiqijiang17
  2

• No Bracken kmer distributions for strain level taxids

  #17 opened 3 years ago by watsonar
  2

• missing clusters_db.10 and 11

  #15 opened 3 years ago by fanhuan
  4

• creating a custom GTDB with user provided MAGs

  #14 opened 3 years ago by Valentin-Bio-zz
  1

• link issues and md5 check sums fails

  #6 opened 3 years ago by slschnorr
  9

• Cannot install the conda environment

  #13 opened 3 years ago by Valentin-Bio-zz
  1

• taxdump page not found

  #4 opened 3 years ago by slschnorr
  4

• FTP site

  #12 opened 3 years ago by alienzj
  4

• lambda expression in `resources` fails to recognize `threads` during dry run

  #10 opened 3 years ago by fanhuan
  5

• TaxIDs and integration of prokaryotic and eukaryotic information

  #7 opened 3 years ago by jaygut
  1

• additional kmer length files

  #8 opened 3 years ago by slschnorr
  1

• error and uncertainty with GTDB_metadata_filter.R

  #5 opened 3 years ago by slschnorr
  3

• CreateCondaEnvironmentException + UnsatisfiableError: The following specifications were found to be incompatible with each other

  #1 opened 3 years ago by marialgk
  3

• Humann3 specifies wrong index for Bowtie2

  #2 opened 3 years ago by BostjanMurovec
  12

• Guidance on NCBI custom genomes download

  #3 opened 4 years ago by NienkeMekkes
  4