Alternative to Novalign?

TreesLab / NCLscan

We have developed a new pipeline, NCLscan, which is rather advantageous in the identification of both intragenic and intergenic "non-co-linear" (NCL) transcripts (fusion, trans-splicing, and circular RNA) from paired-end RNA-seq data.

MIT License

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Alternative to Novalign? #19

Open wolfgangrumpf opened 5 years ago

wolfgangrumpf commented 5 years ago

Is there a way to run NCLscan without using Novalign? Can another aligner be substituted?