Genome assembly

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Revision as of 07:16, 11 July 2010

Softwares


Software	Version	Input	Output	Location(machine/folder)
Newbler	2.3(091027_1459)			panflam,panpyro
Phrap	0.990329(Phrap0.990329_patch)			panflam
Phrap	1.090518			panflam
Consed	090206			panflam
CABOG(celera)	6.1	sanger, 454(.sff), illumina(fastq), fastq		panflam,panpyro
maq	0.7.1	ref:fasta, read:illumina, long read(not good)		panflam,panpyro
abyss	1.2.0	illumina		panflam
SOAPdenovo	1.04	illumina		panflam
Corrector(soap package)	1.00	fasta,fastq		panflam
GapCloser(soap package)	1.10	fasta,fastq		panflam
MIRA		sanger,454,illumina

Dupfinisher
- Downloaded
Polisher
- Can't find...

Logbook

phrap 사용 solexa 조립

read의 이름을 어떻게 변환? manual을 보면 "create a script which translates your read names into St. Louis", 다른 사람들이 만들어 놓은 script는 없나?

다시 addSolexaReads.perl

gnusnah@panflam:~/works/assembly_2010_7_8/SE_PE/consed/edit_dir$ addSolexaReads.perl 454Contigs.ace.1 solexa_files.fof ref.fa

100711 Solexa read 변환

"." 을 N 으로 변환: cat s_3.1.fastq | perl -pi -e 's/\./N/g' > N_s_3.1.fastq

Add solexa reads to Newbler result

gnusnah@panflam:~/works/assembly_2010_7_8/SE_PE/consed/edit_dir$ addSolexaReads.perl 454Contigs.ace.1 solexa_files.fof ref.fa

총 33분 걸림
error - 454Contigs.ace.2 file: 0 -> 하드가 100% 됐었음, 정리 후 다시 실행
다시 error - read에 포함된 "." 가 문제 - 어떻게 해결? "." 가 있는 read 삭제? 삭제할 때는 pair인 read도 함께 삭제? -> "."을 n으로 바꾸면 될지도.

run Newbler PE

runAssembly -o PE -a 50 -l 350 -g -m -ml 20 -cpu 0 -consed ~/db/genome/Eubacteria/APR_2010_PE/GE6FA8204.sff (/home/gnusnah/works/assembly_2010_7_8/)

run Newbler SE

runAssembly -o SE -a 50 -l 350 -g -m -ml 20 -cpu 0 -consed ~/db/genome/Eubacteria/NOV_2009_SE/GIST.SE.sff (/home/gnusnah/works/assembly_2010_7_8/)

add solexa read, doing...

under /home/gnusnah/works/assembly_2010_7_8/consed/

make dir : solexa_dir
- link to fastq (2 paired end file)
make file : edit_dir/solexa_files.fof

Consed Customization

file : /home/gnusnah/.consedrc
add environment : /home/gnusnah/.bashrc

Consed Install

Consed_Install

While customizing phredPhrap, the location of polyphred should be confirmed. Polyphred is not installed. Sent request e-mail.

run Newbler SE + PE

runAssembly -o SE_PE -a 50 -l 350 -g -m -ml 20 -cpu 0 -consed ~/db/genome/Eubacteria/NOV_2009_SE/GIST.SE.sff ~/db/genome/Eubacteria/APR_2010_PE/GE6FA8204.sff (/home/gnusnah/works/assembly_2010_7_8/)

Try Consed

gnusnah@panflam:~/works/assembly_2010_7_8/SE_PE/consed/edit_dir$ ~/tools/UW/consed/consed_linux64bit

phred

add environment : /home/gnusnah/.bashrc PHRED_PARAMETER_FILE=/home/gnusnah/tools/UW/phred/phredpar.dat export PHRED_PARAMETER_FILE