SegataLab/panphlan

Issues

• Duplicated sequences in reference fasta

  #42 opened 3 months ago by robbueck
  0

• I must merge the Pair-ends metagenomic data together, and then starting running the panphlan mapping.

  #41 opened a year ago by allen-zhan340
  0

• Problem with download reference genome from PanPhlAn pangenome database

  #40 opened a year ago by shiangchiet
  0

• panphlan_clean_pangenome.py isn't installed as part of the package

  #39 opened 2 years ago by sterrettJD
  0

• How to import roary pangenome results into panphlan?

  #38 opened 2 years ago by yihandqx
  0

• Meet “OSError: Invalid data stream” when using panphlan_profiling.py

  #19 opened 4 years ago by siriusorignblack
  11

• Index for manual {species}_pangenome.tsv

  #37 opened 3 years ago by Hocnonsense
  0

• Error running panphlan_map

  #20 opened 4 years ago by sanpande
  6

• missing link `How to find and download reference genomes from NCBI?`

  #36 opened 3 years ago by fconstancias
  1

• Error running the sample a second time

  #35 opened 3 years ago by namdeka
  1

• <mpileup> Set max per-file depth to 8000: What is it?

  #33 opened 3 years ago by namdeka
  3

• panphlan_map.py (ERR): bowtie2-align exited with value 134 'std::bad_alloc'

  #32 opened 3 years ago by Gargari
  6

• Duplicate sequence in Cardiobacterium hominis pangenome

  #34 opened 3 years ago by andrewjmc
  2

• Using RAST annotations

  #29 opened 4 years ago by minna-miha
  2

• reference pangenome not available

  #30 opened 4 years ago by xzl0034
  2

• --func_annot

  #27 opened 4 years ago by nick-youngblut
  6

• Lactobacillus case and Lactobacillus paracasei

  #28 opened 4 years ago by qinglong89
  1

• panphlan_download_pangenome.py: panphlan_pangenomes_links.tsv written to cwd

  #25 opened 4 years ago by nick-youngblut
  0

• panphlan_profiling.py: allow user to specify input files

  #24 opened 4 years ago by nick-youngblut
  0

• panphlan bioconda recipe is incomplete

  #23 opened 4 years ago by nick-youngblut
  1

• panphlan_map.py: Cannot set temporary directory location

  #22 opened 4 years ago by nick-youngblut
  5

• panphlan_download_pangenome.py: number of retries

  #21 opened 4 years ago by nick-youngblut
  10

• speed up panphlan_map.py with intervaltree?

  #26 opened 4 years ago by nick-youngblut
  0

• working with mapping files - enquiries

  #18 opened 4 years ago by GaioTransposon
  3

• Duplicated sam header error in panphlan_map.py

  #17 opened 4 years ago by AUAShen
  5

• UniRef90 genes to function

  #15 opened 4 years ago by GaioTransposon
  3

• IndexError: list index out of range

  #16 opened 4 years ago by GaioTransposon
  3

• pangenomes corrupted

  #14 opened 4 years ago by GaioTransposon
  2

• problems with using standard input

  #13 opened 4 years ago by AUAShen
  4

• NameError: name 'randint' is not defined during panphlan_profiling.py

  #5 opened 5 years ago by fconstancias
  7

• Wiki installation

  #11 opened 5 years ago by fbeghini
  0

• Track unknown strains

  #12 opened 5 years ago by termithorbor
  5

• HUMAnN2_CHOCOPhlAn_201901_functional_annotation_mapping.tsv

  #7 opened 5 years ago by fconstancias
  4

• Paired end reads

  #10 opened 5 years ago by andrewjmc
  2

• PanPhlAn RNA-seq using latest version of panphlan

  #8 opened 5 years ago by fconstancias
  7

• about the filename extension

  #6 opened 5 years ago by dytk2134
  4

• Where to download pangenome file of a species?

  #4 opened 5 years ago by lz870718
  6

• NotADirectoryError: [Errno 20] Not a directory: False

  #3 opened 5 years ago by zckoo007
  1

• How to obtain chocophlan pangenome.csv?

  #2 opened 5 years ago by tamburinif
  2