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added new param
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mahulchak committed Jul 6, 2016
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Expand Up @@ -77,7 +77,7 @@ The package contains all necessary components to run quickmerge. We also provide

-l: controls the length cutoff for anchor contigs. A good rule of thumb is to start with the N50 of the 'self_assembly.fasta'. E.g. if the N50 of your self_assembly.fasta is 2Mb. Then use 2000000 as your cutoff. Lowering this value will lead to more merging but may increase the probability of mis-joins.

-ml: controls the minimum length of the alignment to be considered for merging. This is especially helpful for repeat-rich genomes. Default is 0 but 5000 is a good starting point.
-ml: controls the minimum alignment length to be considered for merging. This is especially helpful for repeat-rich genomes. Default is 0 but 5000 is a good starting point.

4. SOME HELPFUL TIPS:

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