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Chorus_perl

A perl implement of Chorus idea. Checkout https://github.com/forrestzhang/Chorus. This project is just for learning purpose. Chorus_perl is by no means to take any credit. All the credits and citatation should refer to https://github.com/forrestzhang/Chorus.

requirement

perl model:

Inline::python
Parallel::ForkManager
BerkeleyDB

external tools:

samtools (http://www.htslib.org/)
bwa (https://sourceforge.net/projects/bio-bwa/files/)
KMC3.0 (http://sun.aei.polsl.pl/kmc)

python:

primer3-py (https://pypi.python.org/pypi/primer3-py)

usage

perl Chorus_perl.pl -gs <genome file> -t <target sequence file>

Options:

        -help              this help message
          -gs              genome sequence file (while genome, including unanchored scaffolds/contigs), MANDATORY
           -t              target sequence file (could be one region or one chromosome. could be whole genome but not recommended),
                           MNADATORY
          -km              pre-calculated kmer profile
          -uk              uniq kmer cutoff, default is 1 for genomic, but if not use genomic for kmer profile, set accordingly
           -s              step of ajacent probe , default is every 5bp.
           -r              max length of repeat nucleotide (AAAA,TTTT...), default is 5
           -a              max number of N or n, default is 1
           -k              length of kmer, default is 17
           -m              running mode,canbe set to highMem and lowMem, default is highMem
           -n              max number of multiple kmers in a probe, default is 4
           -h              max homologous in the genome, default is 0.7
           -p              min tm of probe, default is 37
           -q              max tm for hairpin (htm) of probe, default is 35
           -d              min differences between tm and htm, default is 10
           -e              number of threads, default is 4

run Chorus_perl

Design probe for chr1.fa:

perl Chorus_perl.pl -gs wholeGenome.fa -t chr1.fa -n 3 -e 20