Questions about MaSuRCA assembly program

Question

[arnstrm]

Hi all,

I have few questions about MaSuRCA assembly program and I will greatly appreciate if anyone can clarify these doubts:

1. Do I have to run trimmomatic or any other filtering/trimming tools before I run the assembly? I am asking this because the program already has a inbuilt error correction step.
2. How to specify the overlapping libraries ? The sr-config file asks to provide input library as 1)two_letter_prefix 2)mean 3)stdev 4)fastq 1 5) fastq 2, but negative mean are to specify paired-end reads that are outies (RF) and it won't accept 0 as insert size. Also, is the mean, insert-size or the total size (read length * 2 + insert size)?
3. Do I have to combine similar library types into a single file before putting them in sr-config file or is it OK to specify each library separately?

Thanks very much,

Answer 1

[rtliu]

1. No need to run trimmomatic. the inbuilt error correction step has adapter trimming, error correction, etc.

2. Read the quick start guide e.g.

   PE = aa 180 20 /data/fwd_reads.fastq /data/rev_reads.fastq* The 'mean' and 'stdev' parameters are the library insert average length and standard deviation.

   "JUMP are assumed to be outties <---.--->. If there are any jump libraries that are innies, such as longjump, specify them as JUMP and specify NEGATIVE mean."

   So negative mean is for longjump library, not for paired-end reads.

3. No, you can specify each library per line, e.g. add a new line, supposed 250bp PE library with 30bp stdev

   PE = bb 250 30 /data/fwd_reads_1.fastq /data/rev_reads_1.fastq

Good luck!

[arnstrm]

Thanks very much for answering! I am still not getting the second question. If I have overlapping libraries (miseq) of length 250bp (R1=250bp, R2=250bp), with 50bp overlap, what would be the insert size? will it be the total length (450bp) or insert size (-50bp)?

Thanks once again!

[rtliu]

insert size = 450bp