panphlan
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SegataLab
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
I must merge the Pair-ends metagenomic data together, and then starting running the panphlan mapping. is there any convenient way to map pair-ends metagenomic sequence?
Hi, Thank you for developing this great tool! I am using python 3.9.18 and trying to download reference genomes for a few species from PanPhlAn pangenome database following the Tutorial-3_0...
Hi PanPhlAn team, I was going to use `panphlan_clean_pangenome.py` with to clean a pangenome that I downloaded with PanPhlAn v3.1 and am using for mapping. However, through the conda installed...
Hi, thanks for providing us with the tool for phylogenomic analysis. I am trying to use panphlan to do strain-level analysis on a species which here has more than 2,000...
https://github.com/SegataLab/panphlan/blob/a7846e4ada410fe791ded6297551be96883a7048/panphlan_map.py#L361-L362 Hello and thanks for your code. I'me tring to apply this software to my metagenome analysis, and I've already annote all my MAGs with prodigal followed by mmseqs and...
Hi, Is the tool still being maintained? I get the following error, any idea what is causing it? [mpileup] 1 samples in 1 input files Set max per-file depth to...
I get this error after the step 3 (strain presence/absence) during profiling when I try a different threshold. It was working the first time I tried it. What can be...
The wiki page on profiling shows the output as: ``` sample01 sample04 sample05 sample08 g00001 1 0 1 0 g00002 0 1 1 1 g00003 0 0 0 1 g00003...
In the code: ``` with open(reads_file, mode='r') as IN: for line in IN: words = line.strip().split('\t') # words = CONTIG, POSITION, REFERENCE BASE, COVERAGE, READ BASE, QUALITY contig, position, abundance...
Hey there, I am encountering the following error when running the panphlan_profiling.py script: ``` ... STEP 2. Create coverage matrix [I] Reading mapping result file: MP3_TONGUE_DNA_Rothia_dentocariosa.csv.bz2 [I] Reading mapping result...
