map_reads_to_reference.py – Script for performing assignment of reads against a reference database¶
Description:
Usage: map_reads_to_reference.py [options]
Input Arguments:
Note
[REQUIRED]
- -i, --input_seqs_filepath
- Path to input sequences file
- -r, --refseqs_fp
- Path to reference sequences to search against [default: None]
[OPTIONAL]
- -m, --assignment_method
- Method for picking OTUs. Valid choices are: bwa-short, usearch, bwa-sw, blat, blat-nt. [default: usearch]
- -t, --observation_metadata_fp
- Path to observation metadata (e.g., taxonomy, EC, etc) [default: None]
- -o, --output_dir
- Path to store result file [default: ./<METHOD>_mapped/]
- -e, --evalue
- Max e-value to consider a match [default: 1e-10]
- -s, --min_percent_id
- Min percent id to consider a match [default: 0.75]
- --genetic_code
- ID of genetic code to use for DNA translations (please see http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi) Only valid with -m blat. [default: 11]
- --max_diff
- MaxDiff to consider a match (applicable for -m bwa-short) – see the aln section of “man bwa” for details [default (defined by bwa): 0.04]
- --queryalnfract
- Min percent of the query seq that must match to consider a match (usearch only) [default: 0.35]
- --targetalnfract
- Min percent of the target/reference seq that must match to consider a match (usearch only) [default: 0.0]
- --max_accepts
- Max_accepts value (usearch only) [default: 1]
- --max_rejects
- Max_rejects value to (usearch only) [default: 32]
Output:
Run assignment with usearch using default parameters
map_reads_to_reference.py -i query_nt.fasta -r refseqs_pr.fasta
Run nucleotide versus protein BLAT using default parameters
map_reads_to_reference.py -i query_nt.fasta -r refseqs_pr.fasta -m blat
Run nucleotide versus protein BLAT using scricter e-value threshold
map_reads_to_reference.py -i query_nt.fasta -r refseqs_pr.fasta -o blat_mapped_strict/ -e 1e-70 -m blat
Run nucleotide versus nucleotide BLAT with default parameters
map_reads_to_reference.py -i query_nt.fasta -r refseqs_nt.fasta -m blat-nt
Run assignment with bwa-short using default parameters. bwa-short is intended to be used for reads up to 200bp. WARNING: reference sequences must be dereplicated! No matches will be found to reference sequences which show up multiple times (even if their sequence identifiers are different)!
map_reads_to_reference.py -i query_nt.fasta -r refseqs_nt.fasta -m bwa-short
Run assignment with bwa-sw using default parameters. WARNING: reference sequences must be dereplicated! No matches will be found to reference sequences which show up multiple times (even if their sequence identifiers are different)!
map_reads_to_reference.py -i query_nt.fasta -r refseqs_nt.fasta -m bwa-sw