Spades assembler artifacts? Contigs containing long nt stretches.
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6.8 years ago
fhsantanna ▴ 550

Hi.

I have utilized  Spades software to assemble my pair-ended Miseq data from four different bacteria (multiple species: Lysobacter, Bacillus, Paenibacillus and Rhizobium). In general, this software generated around 100-900 contigs for these bacteria.

But I have noticed that all different assemblies have contigs containing only C's (or A's) with the length of ~130 nts. Also, in a specific species there are long G stretches (100-200 nts) immersed in their contigs.

Do you know how could I discard automaticallly these artifacts?

Thanks in advance.

genome Assembly spades artifacts contigs • 1.7k views
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I utilized the --careful option and much of these sequences were removed, even so there are some contigs with this problem.

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