Well, I'm a newbie of Mugsy, so...hope I'm not asking a stupid question....
I've already have a set of contigs which is done by de novo assembler. Format of these contigs is fasta. Now I want to align these contigs to a reference sequence by using Mugsy. And obtain only single score shown the similarity between contigs and reference sequence.
mugsy --directory /home/H24991180/Mugsy/Velvet/r2 --prefix velvet_r2 contigs.fa Arabidosis_thaliana.ch.fa
Parsing sequences for contigs num_seqs:51179
Parsing sequences for Arabidosis_thaliana num_seqs:5
Starting Nucmer: Sun Sep 22 01:14:14 CST 2013 . Finished Nucmer Sun Sep 22 01:51:51 CST 2013
Starting MUGSYWGA: Sun Sep 22 01:51:51 CST 2013
Finished MUGSYWGA: Sun Sep 22 05:49:26 CST 2013
Final output (MAF format): /home/H24991180/Mugsy/Velvet/r2/velvet_r2.maf
Finished Sun Sep 22 05:49:26 CST 2013
The output of maf file:
maf version=1 scoring=mugsy
a score=43769 label=1 mult=2
s Arabidosis_thaliana.gi|332002898|gb|CP002688.1| 23544873 37605 + 26975502
s contigs.NODE_203395_length_51126_cov_11.976137 5065 40426 - 51218
a score=32893 label=2 mult=2
s Arabidosis_thaliana.gi|330250293|gb|CP002685.1| 3391933 32785 + 19698289
s contigs.NODE_10073_length_33024_cov_248.175110 0 32791 + 33116
I want to know what's the meaning of "score" here ?
And because it only showed identity and score for each contig,how can I get a summarizing values representing the similarity between contigs and reference sequence.
I've searched for hours and can't seem to find a straight answer. Please do help me....thanks!!