ILRI Research Computing

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====== nextalign ======
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.

===== Information =====

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

===== Usage =====

See versions which are available:
<code>$ module avail nextalign</code>

Load one version into your environment and run it:
<code>$ module load nextalign/1.11.0
$ nextalign</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ 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</code>