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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/0.1.7
$ nextalign


Notes from the sysadmin during installation:

$ cd /tmp
$ wget
$ 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
nextalign-software.txt · Last modified: 2021/03/15 10:31 by aorth