DerrickWood/kraken2

Issues

• Custom DB and custom taxonomy (GTDB or similar)

  #884 opened a month ago by osvatic
  0

• Ambiguous bases being included in confidence score calculation

  #878 opened 2 months ago by mcolpus
  1

• kraken2 2.1.9 empty taxonomic level field in k2report

  #883 opened a month ago by GODCALLMEGOD
  1

• 18S, ITS, COI and chloroplast data analysis with kraken2

  #882 opened a month ago by mars188
  0

• Kraken2 classified first read of the pair and not the other each time when both names are supplied

  #861 opened 3 months ago by kaydadaemon
  5

• Kraken 2 finds spurious minimizers after ambiguous regions

  #881 opened 2 months ago by jtnystrom
  0

• Support zstd input

  #877 opened 2 months ago by mbhall88
  0

• Viral Refseq outdated on more than year in comparison with ICTV VMR.39

  #880 opened 2 months ago by igortru
  0

• Merge two Kraken databases?

  #864 opened 3 months ago by Pablo-UY
  2

• Is there a matched names.dmp and nodes.dmp file for the pre-built Kraken2 database

  #848 opened 4 months ago by PandengWang
  4

• Ewquest to provide Kraken2 index for the FDA-ARGOS

  #839 opened 5 months ago by Rohit-Satyam
  8

• Weather could provide a method for comparing multiple samples at once

  #876 opened 3 months ago by PingWang7
  3

• Use of 16S Data with the Kraken2 Database

  #875 opened 3 months ago by christopherwilliamlee
  0

• `k2mask` is only single-threaded even with `--threads` and `OMP_NUM_THREADS` set properly

  #855 opened 3 months ago by hermidalc
  8

• Parameters for database construction and classification with Nanopore v14 chemistry

  #874 opened 3 months ago by rjsorr
  0

• Unable to build db.

  #852 opened 4 months ago by abskumar
  9

• Issue with plusPFP download

  #873 opened 3 months ago by ShaktiprasadM
  1

• How to Extract Specific Genomes or Full-Length rRNA Sequences from kraken2 PlusPF Database

  #872 opened 3 months ago by chenlipeng2019
  0

• Is there a way to extract the kmers of a specific species from the Kraken2 database?

  #871 opened 3 months ago by wangzhichao1990
  0

• Issue with `k2 add-to-library`

  #859 opened 4 months ago by ChillarAnand
  13

• make: *** src: No such file or directory. Stop.

  #870 opened 3 months ago by lauraelf
  3

• Error in kraken2 with taxpasta

  #869 opened 3 months ago by brockels
  3

• Taxon assignment report not adding up to 100%

  #868 opened 3 months ago by antantjuju
  0

• database being used

  #867 opened 3 months ago by chrissy005
  2

• Why is `k2mask` set to use only half the number of available cores?

  #858 opened 4 months ago by hermidalc
  5

• Unable to find k2mask in path, can't mask low-complexity sequences

  #865 opened 3 months ago by zrf-cp
  1

• Avoid sequence ID map to Taxon

  #863 opened 3 months ago by juanjo255
  0

• Species-level 16S kraken2 database?

  #862 opened 3 months ago by DntBScrdDv
  2

• Unable to install Kraken 2 and bracken on my Mac using conda

  #860 opened 3 months ago by chrissy005
  2

• how to update existing build?

  #854 opened 4 months ago by elbriandominguez
  3

• Make `k2` wrapper script available in `$PATH` in the Bioconda `kraken2` package

  #857 opened 4 months ago by hermidalc
  1

• Return of the FTP error- rsync_from_ncbi.pl: unexpected FTP path (new server?)

  #847 opened 4 months ago by Madeleine-Meyer
  6

• scan_fasta_file.pl: unable to determine taxonomy ID for sequence

  #856 opened 4 months ago by amara86
  1

• Missing species in inspect file after database build

  #853 opened 4 months ago by ksavhughes
  1

• can get mapped region in output result?

  #846 opened 4 months ago by jyl-hb
  5

• #No preliminary seqid/taxid mapping files found, aborting.

  #851 opened 4 months ago by SamridhiVerma07
  2

• Test results did not meet expectations

  #849 opened 4 months ago by hedy-ella
  0

• Terminal disappears automatically when runs classification command

  #845 opened 5 months ago by pratibha-kadam
  2

• Kraken2 does not add to the custom library *every* downloaded sequence

  #844 opened 5 months ago by LeandroD94
  6

• How to merge Refseq databases？

  #836 opened 6 months ago by smoothyly
  2

• discrepancy between Kraken results and BLAST hits

  #842 opened 5 months ago by kuldeepmore10
  4

• Low minimizer count in prebuilt NT Database leading to unclassified reads

  #841 opened 5 months ago by remondulos
  0

• Download speed of databases

  #840 opened 5 months ago by bheimbu
  0

• Kraken2 Databases

  #838 opened 5 months ago by hamzaaitabbou96
  0

• Issue with ITS analysis

  #837 opened 6 months ago by christopherwilliamlee
  0

• Assembly unclassified using Kraken2 but can be identified running Blastn

  #835 opened 6 months ago by mbacino
  0

• Number of reads in .kraken2.output.txt, _1.fq and _unclassfied_1.fq inconsistent with reads in input fastq file

  #834 opened 6 months ago by MAlinkous
  3

• Kraken2 custom build skips high identity added fastas

  #833 opened 6 months ago by annabel-dekker
  0

• build_db: error opening taxonomy//nodes.dmp: No such file or directory

  #832 opened 6 months ago by B1991ing
  1

• Using kraken2 to extract/group the read/contigs based on their corresponding taxa (some kind of binning).

  #831 opened 6 months ago by kaydadaemon
  0