Linux command
nextalign 命令
文本
复制后可按需替换文件名、目录或参数。
常用示例
Align sequences to reference
nextalign run --input-ref [reference.fasta] -i [sequences.fasta] -o [aligned.fasta]
Use genome annotation
nextalign run --input-ref [ref.fasta] --input-annotation [genemap.gff3] -i [seqs.fasta] -o [out.fasta]
Output all results to a directory
nextalign run --input-ref [ref.fasta] -i [seqs.fasta] --output-all [output_dir/]
Use a Nextclade dataset instead of individual files
nextalign run --input-dataset [nextstrain/sars-cov-2/wuhan-hu-1/orfs] -i [seqs.fasta] -o [out.fasta]
Set number of threads
nextalign run -j [8] --input-ref [ref.fasta] -i [seqs.fasta] -o [out.fasta]
说明
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. As of Nextclade v3, the standalone Nextalign CLI has been superseded by nextclade run, which provides the same alignment functionality plus additional analysis. Users are encouraged to migrate to nextclade.
参数
- --input-ref _file_
- Reference sequence (FASTA). Required when not using --input-dataset.
- -i, --input _file_
- Input sequences (FASTA).
- -o, --output-fasta _file_
- Output aligned sequences.
- --input-annotation _file_
- Genome annotation (GFF3).
- --input-dataset _name_
- Use a Nextclade dataset (replaces individual --input-ref, --input-annotation).
- --output-all _dir_
- Write all output files to a directory.
- --output-translations _template_
- Output translated protein sequences.
- -j, --jobs _n_
- Number of threads.
- --include-reference
- Include reference sequence in output alignment.
- --in-order
- Output sequences in the same order as input.
FAQ
What is the nextalign command used for?
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. As of Nextclade v3, the standalone Nextalign CLI has been superseded by nextclade run, which provides the same alignment functionality plus additional analysis. Users are encouraged to migrate to nextclade.
How do I run a basic nextalign example?
Run `nextalign run --input-ref [reference.fasta] -i [sequences.fasta] -o [aligned.fasta]` in a terminal, then adjust file names, paths, flags, or remote targets for your system.
What does --input-ref _file_ do in nextalign?
Reference sequence (FASTA). Required when not using --input-dataset.