News and Announcements » – Parallel sequence alignment using PyNAST


A wrapper for the PyNAST option, intended to make use of multicore/multiprocessor environments to perform analyses in parallel.

Usage: [options]

Input Arguments:



-i, --input_fasta_fp
Path to the input fasta file
-o, --output_dir
Path to the output directory


-t, --template_fp
Filepath for template alignment [default: /Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/` <./85_otus.html>`_nast.fasta]
-a, --pairwise_alignment_method
Method to use for pairwise alignments [default: uclust]
-d, --blast_db
Database to blast against [default: created on-the-fly from template_alignment]
-e, --min_length
Minimum sequence length to include in alignment [default: 75% of the median input sequence length]
-p, --min_percent_id
Minimum percent sequence identity to closest blast hit to include sequence in alignment, expressed as a real number between 0 and 100 [default: 75.0]
-O, --jobs_to_start
Number of jobs to start [default: 1]
-R, --retain_temp_files
Retain temporary files after runs complete (useful for debugging) [default: False]
-S, --suppress_submit_jobs
Only split input and write commands file - don’t submit jobs [default: False]
-T, --poll_directly
Poll directly for job completion rather than running poller as a separate job. If -T is specified this script will not return until all jobs have completed. [default: False]
-U, --cluster_jobs_fp
Path to cluster jobs script (defined in qiime_config) [default:]
-W, --suppress_polling
Suppress polling of jobs and merging of results upon completion [default: False]
-X, --job_prefix
Job prefix [default: descriptive prefix + random chars]
-Z, --seconds_to_sleep
Number of seconds to sleep between checks for run completion when polling runs [default: 1]


This results in a multiple sequence alignment (FASTA-formatted).


Align the input file (-i) against using PyNAST and write the output (-o) to $PWD/pynast_aligned_seqs/. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/). -i $PWD/inseqs.fasta -o $PWD/pynast_aligned_seqs/