We got some fosmid sanger sequences (end-sequencing) of metagenomic samples.
My work plan is as the following
1) phred base call
2)data cleaning (trimming off vector fragement, host genomic fragment; trimming off the low quality region). which tools to use, please give me some suggestions.
3) assembly: Tools I can think of phrad, cap3, some people recommended mira.
This is my first time to handling pair end metagenomic sequences. Could you give me some suggestions what kind of things that I need to keep in mind while I am handling this kind of the data set.
My work plan is as the following
1) phred base call
2)data cleaning (trimming off vector fragement, host genomic fragment; trimming off the low quality region). which tools to use, please give me some suggestions.
3) assembly: Tools I can think of phrad, cap3, some people recommended mira.
This is my first time to handling pair end metagenomic sequences. Could you give me some suggestions what kind of things that I need to keep in mind while I am handling this kind of the data set.