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.

• Version: 1.11.0
• Added: March, 2021
• Updated: April, 2022
• Link: https://github.com/nextstrain/nextclade/tree/master/packages/nextalign_cli

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 https://github.com/nextstrain/nextclade/releases/download/1.11.0/nextalign-Linux-x86_64 -O /export/apps/nextalign/1.11.0/bin/nextalign
$ sudo chmod +x /export/apps/nextalign/1.11.0/bin/nextalign