Script to improve long read (pacbio) assemblies
This wrapper script was written to cleanup PacBio assemblies produced with HGAP v3. We used in to assemble the P. cynomolgi assembly, many P. falciparum genomes.
It was also test for Leishmania, where Karen (thanks!) compared her merges with the output of the script, confirming all the edits.
Following step are done: Ignore contigs smaller than 5kb. Delete contigs if they are contained with more than 90% of there overlap (IPA.getOverlap.pl). Merge contigs if the Illumina reads coverage is 50% of the median coverage. (findoverlaps_ver3.pl - Author Susanne Reimering) Abacas2 to order the contigs (at least rename them) icorn2 to correct homopolymer track from the PacBio assembly
You need following package installed and in the path abacas2 - https://github.com/sanger-pathogens/ABACAS2 icorn2 - icorn.sourceforge.net/ : set ICORN2_THREADS=8; export ICORN2_THREADS; circlator - https://github.com/sanger-pathogens/circlator fastaq - https://github.com/sanger-pathogens/Fastaq smalt - http://www.sanger.ac.uk/science/tools/smalt-0 samtools - you know where... bwa - last version with the bwa mem blastall - ncbi distribution that has megablast...
This scripts works well on our computer farm. I adapted it for general use. Certain steps, like the circularization are programmed for Plasmodium. If you have problems to run the script please let me know.
We are happy to announce that ILRA has replaced IPA, which is now deprecated. The use of IPA is discouraged. ILRA is actively maintained and all users looking for support can report issues there.