4.5. assemble_refbased

Reference-based microbial consensus calling. Aligns NGS reads to a singular reference genome, calls a new consensus sequence, and emits: new assembly, reads aligned to provided reference, reads aligned to new assembly, various figures of merit, plots, and QC metrics. The user may provide unaligned reads spread across multiple input files and this workflow will parallelize alignment per input file before merging results prior to consensus calling.

4.5.1. Inputs

4.5.1.1. Required inputs

assemble_refbased.reads_unmapped_bams
Array[File]+ — Default: None
Unaligned reads in BAM format

assemble_refbased.reference_fasta
File — Default: None
Reference genome to align reads to.

4.5.1.2. Other common inputs

assemble_refbased.sample_name
String — Default: basename(reads_unmapped_bams[0],'.bam')
Base name of output files. The 'SM' field in BAM read group headers are also rewritten to this value. Avoid spaces and other filename-unfriendly characters.

assemble_refbased.trim_coords_bed
File? — Default: None
optional primers to trim in reference coordinate space (0-based BED format)

4.5.1.3. Other inputs

Show/Hide

assemble_refbased.align_to_ref.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.10"
???

assemble_refbased.align_to_ref.machine_mem_gb
Int? — Default: None
???

assemble_refbased.align_to_ref.sample_name
String — Default: basename(basename(basename(reads_unmapped_bam,".bam"),".taxfilt"),".clean")
???

assemble_refbased.align_to_self.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.10"
???

assemble_refbased.align_to_self.machine_mem_gb
Int? — Default: None
???

assemble_refbased.align_to_self.sample_name
String — Default: basename(basename(basename(reads_unmapped_bam,".bam"),".taxfilt"),".clean")
???

assemble_refbased.aligner
String — Default: "minimap2"
Read aligner software to use. Options: novoalign, bwa, minimap2. Minimap2 can automatically handle Illumina, PacBio, or Oxford Nanopore reads as long as the 'PL' field in the BAM read group header is set properly (novoalign and bwa are Illumina-only).

assemble_refbased.call_consensus.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.1.10.0"
???

assemble_refbased.call_consensus.machine_mem_gb
Int? — Default: None
???

assemble_refbased.call_consensus.major_cutoff
Float? — Default: 0.5
If the major allele is present at a frequency higher than this cutoff, we will call an unambiguous base at that position. If it is equal to or below this cutoff, we will call an ambiguous base representing all possible alleles at that position.

assemble_refbased.call_consensus.mark_duplicates
Boolean? — Default: false
???

assemble_refbased.call_consensus.min_coverage
Int? — Default: 3
Minimum read coverage required to call a position unambiguous.

assemble_refbased.ivar_trim.docker
String — Default: "andersenlabapps/ivar:1.2.2"
???

assemble_refbased.ivar_trim.machine_mem_gb
Int? — Default: None
???

assemble_refbased.ivar_trim.min_keep_length
Int? — Default: None
Minimum length of read to retain after trimming (Default: 30)

assemble_refbased.ivar_trim.min_quality
Int? — Default: 1
Minimum quality threshold for sliding window to pass (Default: 20)

assemble_refbased.ivar_trim.sliding_window
Int? — Default: None
Width of sliding window for quality trimming (Default: 4)

assemble_refbased.merge_align_to_ref.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.10"
???

assemble_refbased.merge_align_to_ref.reheader_table
File? — Default: None
???

assemble_refbased.merge_align_to_self.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.10"
???

assemble_refbased.merge_align_to_self.reheader_table
File? — Default: None
???

assemble_refbased.novocraft_license
File? — Default: None
The default Novoalign short read aligner is a commercially licensed software that is available in a much slower, single-threaded version for free. If you have a paid license file, provide it here to run in multi-threaded mode. If this is omitted, it will run in single-threaded mode.

assemble_refbased.plot_ref_coverage.bin_large_plots
Boolean — Default: false
???

assemble_refbased.plot_ref_coverage.binning_summary_statistic
String? — Default: "max"
???

assemble_refbased.plot_ref_coverage.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.10"
???

assemble_refbased.plot_ref_coverage.plot_only_non_duplicates
Boolean — Default: false
???

assemble_refbased.plot_ref_coverage.skip_mark_dupes
Boolean — Default: false
???

assemble_refbased.plot_self_coverage.bin_large_plots
Boolean — Default: false
???

assemble_refbased.plot_self_coverage.binning_summary_statistic
String? — Default: "max"
???

assemble_refbased.plot_self_coverage.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.10"
???

assemble_refbased.plot_self_coverage.plot_only_non_duplicates
Boolean — Default: false
???

assemble_refbased.plot_self_coverage.skip_mark_dupes
Boolean — Default: false
???

assemble_refbased.run_discordance.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.10"
???

assemble_refbased.run_discordance.min_coverage
Int — Default: 4
???

assemble_refbased.skip_mark_dupes
Boolean? — Default: false
skip Picard MarkDuplicates step after alignment. This is recommended to be set to true for PCR amplicon based data. (Default: false)

---

Generated using WDL AID (0.1.1)