Index of /examples/bioinformatics/icorn2

Icon  Name                    Last modified      Size  Description
[DIR] Parent Directory - [   ] icorn_job.qsub 09-Oct-2015 09:52 379 [   ] Query.contigs.fa 09-Oct-2015 09:42 53K [   ] PfTEST.fasta 09-Oct-2015 09:42 42K [   ] PfTEST.embl 09-Oct-2015 09:42 86K [   ] PAGIT_test_2.fastq 09-Oct-2015 09:42 4.0M [   ] PAGIT_test_1.fastq 09-Oct-2015 09:42 4.0M

iCORN2 package example

To run iCORN2 at the command line:

scc4% module load samtools/1.2
scc4% module load gatk/3.4-46
scc4% module load smalt/0.7.5
scc4% module load snp-o-matic/3.0
scc4% module load icorn/2.0.95

scc4% perl $ICORN2_HOME/icorn2.sh PAGIT_test 350 Query.contigs.fa 1 3
ICORN2.Query.contigs.fa

Iteration ++++ 1
SMALT mapping parameters are set of following (SMALT_PARAMETER): -y 0.5 -r 0 -x
Current corrections:
#iter perfect1 perfect1% perfect2 perfect2% SNP INS DEL HETERO Rej.SNP Rej.INS Rej.DEL
1 8613 38.28 8842 39.30 10 3 2 0 4 0 0
Iteration ++++ 2
SMALT mapping parameters are set of following (SMALT_PARAMETER): -y 0.5 -r 0 -x
Current corrections:
#iter perfect1 perfect1% perfect2 perfect2% SNP INS DEL HETERO Rej.SNP Rej.INS Rej.DEL
1 8613 38.28 8842 39.30 10 3 2 0 4 0 0
2 8852 39.34 8842 39.30 0 0 0 0 4 0 0
Iteration ++++ 3
SMALT mapping parameters are set of following (SMALT_PARAMETER): -y 0.5 -r 0 -x
Current corrections:
#iter perfect1 perfect1% perfect2 perfect2% SNP INS DEL HETERO Rej.SNP Rej.INS Rej.DEL
1 8613 38.28 8842 39.30 10 3 2 0 4 0 0
2 8852 39.34 8842 39.30 0 0 0 0 4 0 0
3 8852 39.34 8842 39.30 0 0 0 0 4 0 0
To look in into a correction, open the file ending with .1 in artemis and load the gff file onto it...


To submit a job, execute command:
scc4% qsub -P my_project icorn_job.qsub


Manual for icorn:
http://icorn.sourceforge.net/