Phusion2 Files

Unikalow - improve genome assemblies by removing Unique Kmers And Low cOpy Words

(1) Prepare a config file used by SOAPdenovo

http://soap.genomics.org.cn/soapdenovo.html

see test.config

(2) Prepare read files with pair end Illumina data
tagreads_0008_1.fastq
tagreads_0008_2.fastq

Note: you can put as many paired files as you want.

(3) Run Unikalow 
Type the command line with full path:
/turing/solexa/zn1/unikalow/unikalow -kmer 71 -trim 90 test.config test_assembly

(4) Your assembly file:
test_assembly.super.fasta

(5) You can check the screened read files at:
tmp.rununik.????

With the screened reads, you may wish to run the data with your own favorite assemblers.
If not, you can remove the files at this directory.

(6) Selecting Kmer size and trimmed read length:
The Kmer size can be 2-127 and the size is dependent on your read length:

We have these suggestions:

For 2x120 bp reads:
-kmer 71 -trim 110 

For 2x100 bp reads:
-kmer 61 -trim 90

For 2x75 bp reads:
-kmer 51 -trim 70

For 2x35 bp reads:
-kmer 31 -trim 35

For any problems, just send e-mails to 

zn1@sanger.ac.uk