I have few questions about
MaSuRCA assembly program and I will greatly appreciate if anyone can clarify these doubts:
- Do I have to run
trimmomaticor any other filtering/trimming tools before I run the assembly? I am asking this because the program already has a inbuilt error correction step.
- How to specify the
overlapping libraries? The
sr-configfile asks to provide input library as 1)two_letter_prefix 2)mean 3)stdev 4)fastq 1 5) fastq 2, but
negative meanare to specify
paired-endreads that are
outies (RF)and it won't accept
0as insert size. Also, is the mean, insert-size or the total size
(read length * 2 + insert size)?
- Do I have to combine similar library types into a single file before putting them in
sr-configfile or is it OK to specify each library separately?
Thanks very much,