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Scripts to estimate frequency of mutations identified in Contingencies in biofilm adaptation of Mycobacterium tuberculosis (Kernien & Youngblom et al. 2024) in a global dataset of M.tb genomes using a previously described method (Smith et al. 2022).

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Name		Name	Last commit message	Last commit date
Latest commit History 9 Commits
Longer		Longer
Shorter		Shorter
README.md		README.md
cobsSeq.fasta		cobsSeq.fasta
cobsSeqPull.py		cobsSeqPull.py
cobs_search.py		cobs_search.py
mutations.txt		mutations.txt
mutations2.txt		mutations2.txt
mutations3.txt		mutations3.txt

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Mtb_COBS

Scripts to estimate frequency of mutations identified in Contingencies in biofilm adaptation of Mycobacterium tuberculosis (Kernien & Youngblom et al. 2024) in a global dataset of M.tb genomes using a previously described method (Smith et al. 2022). Using a searchable compact bit-sliced signature (COBS) index of bacterial genomes curated from the European Nucleotide Archive (Blackwell et al. 2022). Using a Python interface to search COBS index (Bingmann et al. 2019).

References

https://link.springer.com/chapter/10.1007/978-3-030-32686-9_21#Sec3 (Bingmann et al. 2019)

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001421 (Blackwell et al. 2022)

https://elifesciences.org/articles/78454 (Smith et al. 2022)

Data Source

"661k.cobs_compact" https://ftp.ebi.ac.uk/pub/databases/ENA2018-bacteria-661k/

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Scripts to estimate frequency of mutations identified in Contingencies in biofilm adaptation of Mycobacterium tuberculosis (Kernien & Youngblom et al. 2024) in a global dataset of M.tb genomes using a previously described method (Smith et al. 2022).

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