User Tools

Site Tools



Nextalign is a viral genome sequence alignment algorithm used in Nextclade, ported to C++ and made into the standalone command-line tool.

Nextalign performs pairwise alignment of provided sequences against a given reference sequence using banded local alignment algorithm with affine gap-cost. Band width and rough relative positions are determined through seed matching.



See versions which are available:

$ module avail nextalign

Load one version into your environment and run it:

$ module load nextalign/1.11.0
$ nextalign


Notes from the sysadmin during installation:

$ sudo mkdir -p /export/apps/nextalign/1.11.0/bin
$ sudo wget -O /export/apps/nextalign/1.11.0/bin/nextalign
$ sudo chmod +x /export/apps/nextalign/1.11.0/bin/nextalign
nextalign-software.txt · Last modified: 2022/04/01 08:02 by aorth