newbler ignores minimal read length

[DNAjunk]

Hi

I’ve got a question that came up recently regarding the minimal read length in an assembly.

I have 454 and SOLiD reads (35-50 bases) combined and tried to assemble using the "minlen"-option set to 15 which is the lowest value allowed (default is 50 bases).

However, reads shorter than 50 bases were classified as TooShort and excluded from assembly although most of them align perfectly with the obtained contig (I have reads to assemble upon request).

Many thanks and kind regards,

[flxlex]

The minlen does not have an effect on the assembly when set below 50, unless there are paired end reads among the inputdata...