Scripts to run my assembly pipline.
Steps include:
- filter reads
- assembly
- contamination filtering
- detection and removal of haplotigs
- long read polishing
- short read polishing
- busco validation
Tools used:
- Canu
- BLAST
- Blobtools
- minimap
- bwa
- bioawk
- seqtk
- Racon
- Pilon
- NanoPack