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stajichlab / AAFTF

Automatic Assembly For The Fungi
MIT License
19 stars 4 forks source link

Support single-end and interleaved fastq data #2

Closed hyphaltip closed 2 years ago

hyphaltip commented 5 years ago

Support single ended read data for cleanup and assembly.

Support interleaved read data - may still have to split into fwd and rev but the program should do this not require the user.

hyphaltip commented 5 years ago

This is mostly supported but still some kinks to work out as to whether or not Pilon can be supported or depth of coverage assessment reporting in sourpurge

nextgenusfs commented 5 years ago

I think Pilon requires PE reads.

hyphaltip commented 2 years ago

single end works for many steps and merged reads can be given to spades along with paired end.