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: 0.1.7
• Added: March, 2021
• Link: https://github.com/nextstrain/nextclade/tree/master/packages/nextalign_cli

See versions of nextalign which are available:

$ module avail nextalign

Load one version into your environment and run it:

$ module load nextalign/0.1.7
$ nextalign

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/nextstrain/nextclade/releases/download/nextalign-0.1.7/nextalign-Linux-x86_64
$ chmod +x nextalign-Linux-x86_64
$ sudo mkdir -p /export/apps/nextalign/0.1.7/bin
$ sudo cp nextalign-Linux-x86_64 /export/apps/nextalign/0.1.7/bin/nextalign