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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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Assembly of single cells with spades #1398

Closed beacamara closed 1 month ago

beacamara commented 1 month ago

Description of bug

We have used SPADES to assembly Single-cell data (using --sc parameter). In some of the resulting contigs I have detected terminal redundancy with a size of 127 bp. Surprisingly, this is the the same size of one of the k-mers lengths used by spades during the assembly. Is this an error of spades?

image

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPAdes version: 3.13.0

Operating System

Linux-5.14.21-150400.24.46-default-x86_64-with-glibc2.31

Python Version

Python version: 3.9.12

Method of SPAdes installation

conda

No errors reported in spades.log

asl commented 1 month ago

I have detected terminal redundancy with a size of 127 bp.

It is perfectly fine if the sequence is circular. Have you checked this?