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