nextalign
TLDR
Align sequences to reference
$ nextalign run -r [reference.fasta] -i [sequences.fasta] -o [aligned.fasta]
Use gene annotation$ nextalign run -r [ref.fasta] -m [genemap.gff] -i [seqs.fasta] -o [out.fasta]
Output to directory$ nextalign run -r [ref.fasta] -i [seqs.fasta] -O [output_dir/]
Multiple threads$ nextalign run -j [8] -r [ref.fasta] -i [seqs.fasta] -o [out.fasta]
SYNOPSIS
nextalign run [options]
DESCRIPTION
Nextalign is a viral genome sequence alignment tool. It performs pairwise alignment of viral sequences against a reference and identifies mutations, insertions, and deletions.
Nextalign is part of the Nextclade suite, commonly used for SARS-CoV-2 analysis.
PARAMETERS
-r, --reference file
Reference sequence.-i, --input file
Input sequences.-o, --output-fasta file
Output alignment.-m, --genemap file
Gene annotation (GFF).-O, --output-dir dir
Output directory.-j, --jobs n
Number of threads.
OUTPUT FILES
$ aligned.fasta - Aligned sequences
insertions.csv - Insertion positions
translations/ - Translated proteins
insertions.csv - Insertion positions
translations/ - Translated proteins
CAVEATS
Optimized for viral genomes. Reference must be appropriate. Part of Nextclade ecosystem.
HISTORY
Nextalign was developed at the Nextstrain project, led by Trevor Bedford and Richard Neher, gaining prominence during the COVID-19 pandemic.
