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gbouras13 / dnaapler

Reorients assembled microbial sequences
MIT License
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Feature request: Support for linear bacterial replicons? #82

Open tuspjo opened 3 weeks ago

tuspjo commented 3 weeks ago

Thank you for making and maintaining dnaapler!

Streptomyces and other genera have linear chromosomes and often also linear plasmids.

Multiple genes on these replicons are located in a conserved fashion in relation to each other, why it would be practical to orient the replicons according to genes such as the dnaA gene on the chromosome, or replication genes on plasmids.

If dnaapler could have a --linear flag to not rotate the replicons, but still orient them so the key gene is always on the positive strand, that would aid uniformity of assemblies.

Best,

Tue

gbouras13 commented 3 weeks ago

Hi @tuspjo ,

To be clear, you'd simply want a functionality such that e.g. the dnaA gene would always be on the forward strand, but no actual reorientation (as they are linear?) - I guess that would just involve detecting where the dnaA gene is and reverse complimenting the contig if it is negative stranded. Seems straightforward.

George

tuspjo commented 3 weeks ago

Hi George, Yes, exactly, ensuring dnaA on the forward strand without rotating.

Best,

Tue.