lastz.sh

kmer.R

a <- read.table("./MMJ.freq.stat", skip = 8,  sep = "\t", nrows = 254)
png("./kmer.png",type="cairo")
head(a)
plot(a[,1], a[,3]*100,
        xlim = c(0,200),
        ylim = c(0,5),
        col  = "darkblue",
        type = "l",
        lty  = 1,
        xlab = "Sequencing Depth (X)",
        ylab = "Percent (%)",
        main = "Kmer Depth Distribution Curve")
#a <- read.table("./corr/MMJ.freq.stat", skip = 8,  sep = "\t", nrows = 254)
#lines(a[,1],a[,3]*100,col="cyan3",type="l",lty=1,lwd=1.5)
#abline(v=55,col="red",lty=2)
#abline(v=60,col="magenta",lty=2)
#legend("topright",legend=c("Raw","Corr"),col=c("darkblue","cyan3"),lty=c(1,1))
dev.off()

kmer.sh

# work.sh
nohup /data/tanhao/lib/SOAPec_v2.01/bin/KmerFreq_AR -k 17 -t 4 -c -1 -q 33 -p MMJ read.lst >>kmerfreq.cout 2>kmerfreq.cerr &
nohup perl /data/software/Survey/sh4kmer_v1.2.pl -l read.lst -k 17 -Dt 1 -n RSJ &
nohup /data/tanhao/lib/SOAPec_v2.01/bin/Corrector_AR -k 17 -l 45 -Q 33 -t 4 MMJ.freq.cz MMJ.freq.cz.len read.lst >corr.cout 2>corr.cerr &

work.sh

/data/tanhao/dev/alignment/lastz-distrib-1.02.00/src/lastz CM001538.fasta IG1.fa[multi]  --ambiguous=iupac --masking=50 --strand=both --seed=14of22  --gfextend --chain --gapped --format=general:name1,length1,zstart1,end1,strand1,size1,name2,length2,zstart2+,end2+,strand2,size2,identity,coverage,continuity,text1,text2 >IG1.fa.CM001538.fasta.tab
/data/tanhao/dev/alignment/lastz-distrib-1.02.00/src/lastz genome.fasta[multi] IG1.fa[multi]  --ambiguous=iupac --masking=50 --strand=both --seed=14of22  --gfextend --chain --gapped --format=general:name1,length1,zstart1,end1,strand1,size1,name2,length2,zstart2+,end2+,strand2,size2,identity,coverage,continuity,text1,text2 >IG1.fa.genome.fasta.tab
/data/tanhao/dev/alignment/lastz-distrib-1.02.00/src/lastz CM001538.fasta MP-10.fa[multi]  --ambiguous=iupac --masking=50 --strand=both --seed=14of22  --gfextend --chain --gapped --format=general:name1,length1,zstart1,end1,strand1,size1,name2,length2,zstart2+,end2+,strand2,size2,identity,coverage,continuity,text1,text2 >MP-10.fa.CM001538.fasta.tab
/data/tanhao/dev/alignment/lastz-distrib-1.02.00/src/lastz genome.fasta[multi] MP-10.fa[multi]  --ambiguous=iupac --masking=50 --strand=both --seed=14of22  --gfextend --chain --gapped --format=general:name1,length1,zstart1,end1,strand1,size1,name2,length2,zstart2+,end2+,strand2,size2,identity,coverage,continuity,text1,text2 >MP-10.fa.genome.fasta.tab
/data/tanhao/dev/alignment/lastz-distrib-1.02.00/src/lastz CM001538.fasta WCFS1.fa  --ambiguous=iupac --masking=50 --strand=both --seed=14of22  --gfextend --chain --gapped --format=general:name1,length1,zstart1,end1,strand1,size1,name2,length2,zstart2+,end2+,strand2,size2,identity,coverage,continuity,text1,text2 >WCFS1.fa.CM001538.fasta.tab
/data/tanhao/dev/alignment/lastz-distrib-1.02.00/src/lastz genome.fasta[multi] WCFS1.fa  --ambiguous=iupac --masking=50 --strand=both --seed=14of22  --gfextend --chain --gapped --format=general:name1,length1,zstart1,end1,strand1,size1,name2,length2,zstart2+,end2+,strand2,size2,identity,coverage,continuity,text1,text2 >WCFS1.fa.genome.fasta.tab