StrainFinder

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Query regarding Strain Finder

1

Hello, I would like to know if this tool gives the output file containing relative abundances of strains per sample. Thank you

sahilrishav2

Filtering based on coverage

1

Hi, In the preprocessing script 5.filter_np.py, should the filter be `cov != 0` instead? https://github.com/cssmillie/StrainFinder/blob/745a20a6633c53fa5210ae37912d667b6e3645e7/preprocess/5.filter_np.py#L96

lch14forever

Pre-processing issue

2

Using the AMPHORA files in the paper, and applying it to my own data, I've encountered an error with python 5.filter_np.py python 5.filter_np.py --aln all_alignments.cPickle --map /home1/cseto/StrainFinderFiles/bact.meta.txt --samples samples.txt >...

ctseto

Hi, How to deal with the pair end reads in the preprocessing script?

lixin6135

Hello, I had a question about gene content differences between the reference genome and the identified strain. StrainFinder identifies strains based on read mapping to a reference genome. It generates...

cliffbueno