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.. _map_reads_to_reference:
.. index:: map_reads_to_reference.py
*map_reads_to_reference.py* -- Script for performing assignment of reads against a reference database
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
**Usage:** :file:`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
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