<p>Hi all,</p>

<p>I have few questions about <code>MaSuRCA </code>assembly program and I will greatly appreciate if anyone can clarify these doubts:</p>

<ol>
	<li>Do I have to run <code>trimmomatic</code> 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.</li>
	<li>How to specify the <code>overlapping libraries </code>? The <code>sr-config</code> file asks to provide input library as 1)two_letter_prefix 2)mean 3)stdev 4)fastq 1 5) fastq 2, but <code>negative mean</code> are to specify <code>paired-end</code> reads that are <code>outies (RF)</code> and it won&#39;t accept <code>0</code> as insert size. Also, is the mean, insert-size or the total size <code>(read length * 2 + insert size)</code>?</li>
	<li>Do I have to combine similar library types into a single file before putting them in <code>sr-config</code> file or is it OK to specify each library separately?</li>
</ol>

<p>Thanks very much,</p>

1. No need to run trimmomatic. the inbuilt error correction step has adapter trimming, error correction, etc.
2. Read [the quick start guide][1] 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!

 [1]: ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA_QuickStartGuide.pdf