AMOS & BAMBUS program experience sharing and general user guide.

Patrick · 09-04-2009, 03:06 AM

Hi,

Anybody willing to share the experience of using AMOS & BAMBUS program?
Can give the general explanation about this two program and general user guide of these two program?
Thanks a lot for sharing and advise

niazi84@hotmail.com · 02-15-2010, 03:32 AM

HI Patrick,

Did you get any assistance about AMOS. I am at the same position when you did this post. Any help you can do?

Patrick · 02-15-2010, 04:02 PM

Hi,

I just subscribe with the AMOS help. I learning from there now. What problem you have facing now? Anything I can help you too? Maybe we face the same situation too.

niazi84@hotmail.com · 02-15-2010, 04:10 PM

i have installed AMOS but i dont know how to make relevant input formats from illumina reads and reference sequence.

jjohnson · 02-18-2010, 05:14 PM

Adnan,

AMOS is a pretty large suite of tools, what are you trying to do more specifically, maybe I can share some war stories if I know where to start.

niazi84@hotmail.com · 02-19-2010, 01:41 AM

Thanks johnson. I am actually intending to do comparative assembly of bacterial strain whose data is from illumina GA2 with 75bp of reads. The data was in scarf format and i converted it into standard fastq format. Now the thing is that AMOScmp-shortreads takes two inputs .1con and .afg. How to convert reference sequence to .1con? And which steps should i follow till final assembly, viewing and validation? Thanks

niazi84@hotmail.com · 02-19-2010, 08:36 AM

Also how i convert paired end reads in .afg format since nowhere on AMOS pages is mentioned about paired end reads conversion. I am gone mad in this, no help on the web and at AMOS-help.

Kasycas · 06-14-2010, 06:59 AM

Hi niazi84@hotmail.com,

Did you find out about this reference file? I can't find much info anywhere about it!

Thanks,

Kasycas

catfisher · 07-08-2010, 03:28 PM

I got an error when I make files for Bambus, can anybody give help? Thanks,
The error is bellow:

for i in src doc ;do cd $i ; make all; cd .. ; done
make[1]: Entering directory `/home/ngs/SL/software/bambus-2.33/src'
for i in IO DotLib TIGR_Foundation_CC grommit ;do cd $i ; make all; cd .. ; done
make[2]: Entering directory `/home/ngs/SL/software/bambus-2.33/src/IO'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/ngs/SL/software/bambus-2.33/src/IO'
make[2]: Entering directory `/home/ngs/SL/software/bambus-2.33/src/DotLib'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/ngs/SL/software/bambus-2.33/src/DotLib'
make[2]: Entering directory `/home/ngs/SL/software/bambus-2.33/src/TIGR_Foundation_CC'
g++ -D_HAS_GETOPT -c -o ConfigFile.o ConfigFile.cc
ConfigFile.cc: In member function ‘void ConfigFile:

arseConfig()’:
ConfigFile.cc:113: error: ‘strlen’ was not declared in this scope
make[2]: *** [ConfigFile.o] Error 1
make[2]: Leaving directory `/home/ngs/SL/software/bambus-2.33/src/TIGR_Foundation_CC'
make[2]: Entering directory `/home/ngs/SL/software/bambus-2.33/src/grommit'
g++ -I../TIGR_Foundation_CC/ -g -c grommit.cc
grommit.cc: In function ‘int main(int, char**)’:
grommit.cc:236: warning: format ‘%s’ expects type ‘char*’, but argument 3 has type ‘char (*)[1024]’
grommit.cc:317: error: ‘abort’ was not declared in this scope
make[2]: *** [grommit.o] Error 1
make[2]: Leaving directory `/home/ngs/SL/software/bambus-2.33/src/grommit'
make[1]: Leaving directory `/home/ngs/SL/software/bambus-2.33/src'
make[1]: Entering directory `/home/ngs/SL/software/bambus-2.33/doc'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ngs/SL/software/bambus-2.33/doc'

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09-04-2009, 03:06 AM	#1
Patrick Member Location: Malaysia Join Date: Mar 2009 Posts: 27	AMOS & BAMBUS program experience sharing and general user guide. Hi, Anybody willing to share the experience of using AMOS & BAMBUS program? Can give the general explanation about this two program and general user guide of these two program? Thanks a lot for sharing and advise

02-15-2010, 03:32 AM	#2
niazi84@hotmail.com Member Location: Uppsala Join Date: Jan 2010 Posts: 25	HI Patrick, Did you get any assistance about AMOS. I am at the same position when you did this post. Any help you can do? __________________ ~Adnan~

02-15-2010, 04:10 PM	#4
niazi84@hotmail.com Member Location: Uppsala Join Date: Jan 2010 Posts: 25	i have installed AMOS but i dont know how to make relevant input formats from illumina reads and reference sequence. __________________ ~Adnan~

02-18-2010, 05:14 PM	#5
jjohnson Member Location: Washington DC Metro Area Join Date: Aug 2009 Posts: 20	Adnan, AMOS is a pretty large suite of tools, what are you trying to do more specifically, maybe I can share some war stories if I know where to start. __________________ Justin H. Johnson \| Twitter: @BioInfo \| LinkedIn: http://bit.ly/LIJHJ \| EdgeBio

02-15-2010, 04:02 PM	#3
Patrick Member Location: Malaysia Join Date: Mar 2009 Posts: 27	Hi, I just subscribe with the AMOS help. I learning from there now. What problem you have facing now? Anything I can help you too? Maybe we face the same situation too.

02-19-2010, 01:41 AM	#6
niazi84@hotmail.com Member Location: Uppsala Join Date: Jan 2010 Posts: 25	Thanks johnson. I am actually intending to do comparative assembly of bacterial strain whose data is from illumina GA2 with 75bp of reads. The data was in scarf format and i converted it into standard fastq format. Now the thing is that AMOScmp-shortreads takes two inputs .1con and .afg. How to convert reference sequence to .1con? And which steps should i follow till final assembly, viewing and validation? Thanks __________________ ~Adnan~

02-19-2010, 08:36 AM	#7
niazi84@hotmail.com Member Location: Uppsala Join Date: Jan 2010 Posts: 25	Also how i convert paired end reads in .afg format since nowhere on AMOS pages is mentioned about paired end reads conversion. I am gone mad in this, no help on the web and at AMOS-help. __________________ ~Adnan~

06-14-2010, 06:59 AM	#8
Kasycas Member Location: Dublin, Ireland Join Date: Sep 2009 Posts: 22	Hi niazi84@hotmail.com, Did you find out about this reference file? I can't find much info anywhere about it! Thanks, Kasycas

07-08-2010, 03:28 PM	#9
catfisher Member Location: Auburn Join Date: Mar 2010 Posts: 10	I got an error when I make files for Bambus, can anybody give help? Thanks, The error is bellow: for i in src doc ;do cd $i ; make all; cd .. ; done make[1]: Entering directory `/home/ngs/SL/software/bambus-2.33/src' for i in IO DotLib TIGR_Foundation_CC grommit ;do cd $i ; make all; cd .. ; done make[2]: Entering directory `/home/ngs/SL/software/bambus-2.33/src/IO' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/home/ngs/SL/software/bambus-2.33/src/IO' make[2]: Entering directory `/home/ngs/SL/software/bambus-2.33/src/DotLib' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/home/ngs/SL/software/bambus-2.33/src/DotLib' make[2]: Entering directory `/home/ngs/SL/software/bambus-2.33/src/TIGR_Foundation_CC' g++ -D_HAS_GETOPT -c -o ConfigFile.o ConfigFile.cc ConfigFile.cc: In member function ‘void ConfigFile:arseConfig()’: ConfigFile.cc:113: error: ‘strlen’ was not declared in this scope make[2]: * [ConfigFile.o] Error 1 make[2]: Leaving directory `/home/ngs/SL/software/bambus-2.33/src/TIGR_Foundation_CC' make[2]: Entering directory `/home/ngs/SL/software/bambus-2.33/src/grommit' g++ -I../TIGR_Foundation_CC/ -g -c grommit.cc grommit.cc: In function ‘int main(int, char)’: grommit.cc:236: warning: format ‘%s’ expects type ‘char’, but argument 3 has type ‘char ()[1024]’ grommit.cc:317: error: ‘abort’ was not declared in this scope make[2]: *** [grommit.o] Error 1 make[2]: Leaving directory `/home/ngs/SL/software/bambus-2.33/src/grommit' make[1]: Leaving directory `/home/ngs/SL/software/bambus-2.33/src' make[1]: Entering directory `/home/ngs/SL/software/bambus-2.33/doc' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/home/ngs/SL/software/bambus-2.33/doc'