SegataLab panphlan issues

SegataLab / panphlan

PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples

MIT License

41 stars 6 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

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

#41 allen-zhan340 opened 7 months ago
0
Problem with download reference genome from PanPhlAn pangenome database

#40 shiangchiet opened 10 months ago
0
panphlan_clean_pangenome.py isn't installed as part of the package

#39 sterrettJD opened 1 year ago
0
How to import roary pangenome results into panphlan?

#38 yihandqx opened 1 year ago
0
Index for manual {species}_pangenome.tsv

#37 Hocnonsense opened 2 years ago
0
missing link `How to find and download reference genomes from NCBI?`

#36 fconstancias closed 2 years ago
1
Error running the sample a second time

#35 namdeka opened 2 years ago
1
Duplicate sequence in Cardiobacterium hominis pangenome

#34 andrewjmc closed 2 years ago
2
<mpileup> Set max per-file depth to 8000: What is it?

#33 namdeka closed 2 years ago
3
panphlan_map.py (ERR): bowtie2-align exited with value 134 'std::bad_alloc'

#32 Gargari closed 2 years ago
6
Prevent Panphlan from rejecting all mapped reads when the --th_mismat…

#31 fplazaonate closed 3 years ago
2
reference pangenome not available

#30 xzl0034 closed 3 years ago
2
Using RAST annotations

#29 minna-miha closed 3 years ago
2
Lactobacillus case and Lactobacillus paracasei

#28 qinglong89 closed 3 years ago
1
--func_annot

#27 nick-youngblut opened 3 years ago
6
speed up panphlan_map.py with intervaltree?

#26 nick-youngblut opened 3 years ago
0
panphlan_download_pangenome.py: panphlan_pangenomes_links.tsv written to cwd

#25 nick-youngblut closed 3 years ago
0
panphlan_profiling.py: allow user to specify input files

#24 nick-youngblut closed 3 years ago
0
panphlan bioconda recipe is incomplete

#23 nick-youngblut closed 3 years ago
1
panphlan_map.py: Cannot set temporary directory location

#22 nick-youngblut closed 3 years ago
5
panphlan_download_pangenome.py: number of retries

#21 nick-youngblut closed 3 years ago
10
Error running panphlan_map

#20 sanpande opened 3 years ago
6
Meet “OSError: Invalid data stream” when using panphlan_profiling.py

#19 siriusorignblack closed 3 years ago
11
working with mapping files - enquiries

#18 GaioTransposon closed 3 years ago
3
Duplicated sam header error in panphlan_map.py

#17 AUAShen closed 3 years ago
5
IndexError: list index out of range

#16 GaioTransposon closed 3 years ago
3
UniRef90 genes to function

#15 GaioTransposon closed 3 years ago
3
pangenomes corrupted

#14 GaioTransposon closed 3 years ago
2
problems with using standard input

#13 AUAShen closed 3 years ago
4
Track unknown strains

#12 termithorbor closed 4 years ago
5
Wiki installation

#11 fbeghini closed 4 years ago
0
Paired end reads

#10 andrewjmc closed 4 years ago
2
Added setup.py installer for PyPi package

#9 fbeghini closed 4 years ago
0
PanPhlAn RNA-seq using latest version of panphlan

#8 fconstancias closed 4 years ago
7
HUMAnN2_CHOCOPhlAn_201901_functional_annotation_mapping.tsv

#7 fconstancias closed 4 years ago
4
about the filename extension

#6 dytk2134 closed 4 years ago
4
NameError: name 'randint' is not defined during panphlan_profiling.py

#5 fconstancias opened 4 years ago
7
Where to download pangenome file of a species?

#4 lz870718 closed 4 years ago
6
NotADirectoryError: [Errno 20] Not a directory: False

#3 zckoo007 closed 4 years ago
1
How to obtain chocophlan pangenome.csv?

#2 tamburinif closed 4 years ago
2
Dev leo

#1 leonarDubois closed 4 years ago
1