Download Latest Version inGAP-sf1.02.zip (79.1 kB)
Email in envelope

Get an email when there's a new version of ingap-sf

Home
Name Modified Size InfoDownloads / Week
readme.txt 2016-11-10 1.4 kB
0
testData.zip 2016-11-10 273.8 MB
0
inGAP-sf1.02.zip 2016-11-10 79.1 kB
0
inGAP-sf1.02-withData.zip 2016-11-10 273.8 MB
0
inGAP-sf-v1.00.tar.bz2 2016-06-20 4.7 MB
0
Totals: 5 Items   552.3 MB 0 
**********************
*                    *
* BRIEF INSTRUCTIONS *
*                    *
**********************

The file 'inGAP-sf1.02-withData.zip' contains 270MB test dataset, which contains reference genome, contig, blast output for contig alignment, reads mapping result, contig connection, nucmer output for contig alignment. After downloading the package 'inGAP-sf1.02-withData.zip', the users can perform test assembly as follows:

	unzip inGAP-sf1.02-withData.zip
	cd inGAP-sf1.02
	sh ./setup.sh # change to 'sh ./setupForMac.sh' for macOS user
	perl inGAP-sf.pl config.txt -silent

The file 'inGAP-sf1.02.zip' only contains the main program. Test data is in the file 'testData.zip', and the users need to unzip it and put it in the folder '/inGAP-sf1.02/testData' before performing test assembly.

The detail usage is contained in the file 'MANUAL.txt'.

**********************
*                    *
*     CHANGE LOG     *
*                    *
**********************

The latest version of inGAP-sf is 1.02.

Changes:
1. Add some important logs and intermediate output.
2. Fix some bugs including 'out of bound', 'empty hash', 'unlimited search', etc.
3. Reconstruct data structure of route.
4. Optimize two module to reduce time consumption.
5. Optimize pre-scaffold creation strategy.
6. Optimize route merging strategy.
7. Remove mismatch overlapped contigs.
Source: readme.txt, updated 2016-11-10