BIGrat Files

Package:

BIGrat_1.0/
|-- BIGrat.sh
|-- Readme
|-- req_454Reassembly.pl
|-- req_combine_contig.pl
|-- req_process_454PairAlign.pl
`-- test
    |-- 1x.sff
    `-- reference.fna

Note:

The four files should be in the same directory. 

use "chmod a+x *.pl *.sh" to make them executalbe.

make sure the perl executalbe path is "/usr/bin/perl". if not, change the perl files with the correct perl path.
check it with "which perl". 

the SFF_DIR should including only the sff files used in this assemlby.


Requires:

Linux system with basic command such as "awk, sed, sort", if there any problem, please check you system command
and then change the BIGrat.sh according to your system.


Test:
this package includes a test reference and 1x data, input the following commonds:

"runMapping -gref -o newbler1x test/reference.fna test/1x.sff && \
 ./BIGrat.sh <BIGrat_1.0_PATH>/test/newbler1x <BIGrat_1.0_PATH>/test/reference.fna <BIGrat_1.0_PATH>/test/1x.sff 500 & "

Change BIGrat_1.0_PATH to your install_PATH.

Output:

../cp/tmp/newbler1x/
|-- 454AllContigs.fna
...................
...................
|-- Gapfill_500
|   |-- 454AllContigs.fna2
|   |-- 454New_AllContig.fna
|   |-- 454New_LargeContig.fna
|   |-- 454PairAlign.index
|   |-- Gfill.fasta
|   |-- g454PairAlign.txt
|   |-- g454PairAlign_sort.txt
|   |-- gaps.list
|   |-- gaps.reads
|   |-- gaps.sff
|   |-- pre_ncontig.fna
|   `-- ref.fasta


the last combined assembled result is included in the "454New_AllContig.fna" file. 

BUG report:

Any problem can contact with Tongwu Zhang with email: zhangtw@big.ac.cn