lastZconfig

# Write you comments here with "#"
# You can write all lastz parameters here EXECPT --output (if you wanna change it then see script line number 84)
# Do not use seq.fa[multiple], this script do it by one chromosome/scaffolds/contig/sequence at a time
# The outfile will be named after each fasta sequence name:  seeALN_<name>.lz
# Write all command in newline
# You can find detail of parameters here http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html

#For chain only
--chain

#Outfile format ‑‑format=general for tabbed file; 
#Use can also use plotted using the ‑‑format=rdotplot output option and the R statistical package.
--format=general- 
--progress

#Identity here
--identity=90

#Coverage
#‑‑coverage=90

#Ambiguous to take care of N or ambiguous=n
--ambiguous=iupac

#Using ‑‑step=10, we will only be looking for seeds at every 10th base
#‑‑step=10

#Use ‑‑exact=20 so that a 20-base exact match is required to qualify as an HSP
#‑‑exact=20

#The stricter ‑‑match=1,5. This scores matching bases as +1 and mismatches as −5
#‑‑match=1,5

#Check the trand  ‑‑strand=minus  ‑‑strand=plus
#‑‑strand=both