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Hello, i am studing ABySS and i need some help to understand some steps that it does. I was reading abyss presenation of abyss that i came across here:
I would like to ask some stuff that i really need to understand.
1) From the slides i read that the assembly process can be diveded in 2
stages. When abyss-pe is executed both stages take place, isnt it?
When abyss (single end) take place only the first take place?
2)About the 2 stage in understan that: KAligner aligns the contigs
that have k or more same bases?
Then ParseAligns is said that "Generate an empirical fragment-size
distribution using the paired reads that align to the same contig".
What this means? It means that used pair end information to find out
the contigs location? Can you explain me in other words? This happens
only when pe parameter is used? When i use only the parameter lib this
step took place?
3) DistanceEst is using the pair end information to fidn the distance
between 2 contigs? A pair end read that overlap with 2 different
contigs that the dont overlap between them defines the distance
between these 2 contigs? Can you explain me in short the shape? I dont
get it.. Also here this step happens when pe parameter is used?
4)In which way the results of DistanceEst are used to find paths in
the adjacency graph?
5)In merging overlapping paths the blue line is for 2 contigs that
they dont overlap. Althoug are they merged?
6)As i am making a study in ABySS does it has some
requirements for its installation? A minimun memory that need. Can be
installed in a 32bit system? Is there any place that the requirements
are written because i couldnt find one.
I would be grateful if someone could answer me as i need this help a lot.
Thanks
I would like to ask some stuff that i really need to understand.
1) From the slides i read that the assembly process can be diveded in 2
stages. When abyss-pe is executed both stages take place, isnt it?
When abyss (single end) take place only the first take place?
2)About the 2 stage in understan that: KAligner aligns the contigs
that have k or more same bases?
Then ParseAligns is said that "Generate an empirical fragment-size
distribution using the paired reads that align to the same contig".
What this means? It means that used pair end information to find out
the contigs location? Can you explain me in other words? This happens
only when pe parameter is used? When i use only the parameter lib this
step took place?
3) DistanceEst is using the pair end information to fidn the distance
between 2 contigs? A pair end read that overlap with 2 different
contigs that the dont overlap between them defines the distance
between these 2 contigs? Can you explain me in short the shape? I dont
get it.. Also here this step happens when pe parameter is used?
4)In which way the results of DistanceEst are used to find paths in
the adjacency graph?
5)In merging overlapping paths the blue line is for 2 contigs that
they dont overlap. Althoug are they merged?
6)As i am making a study in ABySS does it has some
requirements for its installation? A minimun memory that need. Can be
installed in a 32bit system? Is there any place that the requirements
are written because i couldnt find one.
I would be grateful if someone could answer me as i need this help a lot.
Thanks