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 of nextalign which are available:
$ module avail nextalign
Load one version into your environment and run it:
$ module load nextalign/1.3.0 $ nextalign
Notes from the sysadmin during installation:
$ sudo mkdir -p /export/apps/nextalign/1.3.0/bin $ sudo wget https://github.com/nextstrain/nextclade/releases/download/1.3.0/nextalign-Linux-x86_64 -O /export/apps/nextalign/1.3.0/bin/nextalign $ sudo chmod +x /export/apps/nextalign/1.3.0/bin/nextalign