ismapper

Tags: bacteria mobile-elements insertion-sequences mapping structural-variation ismapper sample-scope

Identify insertion sites and orientation of mobile genetic elements.

Uses ISMapper to identify the position and orientation of specific insertion sequences (IS) in a bacterial genome. It works by mapping paired-end reads to a library of IS queries and a reference genome to determine where the IS elements are located relative to the reference coordinates.

Uses explicit positional record fields for reads:

• Input: record(meta, r1, r2) where each read slot is Path

Inputs

record (
    meta: Record,
    r1: Path,
    r2: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
r1	Path	Illumina R1 reads (paired-end)
r2	Path	Illumina R2 reads (paired-end)

reference: Path
query: Path

Name	Type	Description
reference	Path	Reference genome in GenBank format (*.gbk) to map insertion sites against
query	Path	FASTA file containing the insertion sequences to search for

Outputs

record (
    meta: Record,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

ISMapper Parameters

Parameter	Type	Default	Description
--reference	string		Reference genome for typing against in GenBank format
--insertions	string		Multifasta file with insertion sequence(s) to be mapped to
--ismapper_min_clip	integer	10	Minimum size for softclipped region to be extracted from initial mapping
--ismapper_max_clip	integer	30	Maximum size for softclipped regions to be included
--ismapper_cutoff	integer	6	Minimum depth for mapped region to be kept in bed file
--ismapper_novel_gap_size	integer	15	Distance in base pairs between left and right flanks to be called a novel hit
--ismapper_min_range	number	0.9	Minimum percent size of the gap to be called a known hit
--ismapper_max_range	number	1.1	Maximum percent size of the gap to be called a known hit
--ismapper_merging	integer	100	Value for merging left and right hits in bed files together to simply calculation of closest and intersecting regions
--ismapper_all	boolean	false	Switch on all alignment reporting for bwa
--ismapper_minqual	integer	30	Mapping quality score for bwa

Used By

Subworkflows

• ismapper - Identify transposase insertion sites in bacterial genomes.

Workflows

• ismapper - Identify insertion sequence positions in bacterial genomes.

Citations

If you use this in your analysis, please cite the following.

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• ISMapper
  Hawkey J, Hamidian M, Wick RR, Edwards DJ, Billman-Jacobe H, Hall RM, Holt KE ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data. BMC Genomics 16, 667 (2015)

Source

View source on GitHub

Version

ISMAPPER:
    - ismapper: 2.0.2