4.4. assemble_denovo

4.4.1. Inputs

4.4.1.1. Required inputs

assemble_denovo.reads_unmapped_bam
File — Default: None
???

assemble_denovo.reference_genome_fasta
Array[File]+ — Default: None
After denovo assembly, large contigs are scaffolded against a reference genome to determine orientation and to join contigs together, before further polishing by reads. You must supply at least one reference genome (all segments/chromomes in a single fasta file). If more than one reference is provided, contigs will be scaffolded against all of them and the one with the most complete assembly will be chosen for downstream polishing.

assemble_denovo.trim_clip_db
File — Default: None
???

4.4.1.2. Other inputs

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

assemble_denovo.assemble.machine_mem_gb
Int? — Default: None
???

assemble_denovo.assemble.spades_min_contig_len
Int? — Default: 0
???

assemble_denovo.assemble.spades_n_reads
Int? — Default: 10000000
???

assemble_denovo.assembler
String — Default: "spades"
???

assemble_denovo.call_isnvs
Boolean — Default: false
???

assemble_denovo.deplete_blastDbs
Array[File] — Default: []
Optional list of databases to use for blastn-based depletion. Sequences in fasta format will be indexed on the fly, pre-blast-indexed databases may be provided as tarballs.

assemble_denovo.deplete_bmtaggerDbs
Array[File] — Default: []
Optional list of databases to use for bmtagger-based depletion. Sequences in fasta format will be indexed on the fly, pre-bmtagger-indexed databases may be provided as tarballs.

assemble_denovo.deplete_bwaDbs
Array[File] — Default: []
Optional list of databases to use for bwa mem-based depletion. Sequences in fasta format will be indexed on the fly, pre-bwa-indexed databases may be provided as tarballs.

assemble_denovo.deplete_taxa.clear_tags
Boolean? — Default: false
???

assemble_denovo.deplete_taxa.cpu
Int? — Default: 8
???

assemble_denovo.deplete_taxa.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.10.0"
???

assemble_denovo.deplete_taxa.machine_mem_gb
Int? — Default: None
???

assemble_denovo.deplete_taxa.query_chunk_size
Int? — Default: None
???

assemble_denovo.deplete_taxa.tags_to_clear_space_separated
String? — Default: "XT X0 X1 XA AM SM BQ CT XN OC OP"
???

assemble_denovo.filter_to_taxon.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.10.0"
???

assemble_denovo.filter_to_taxon.error_on_reads_in_neg_control
Boolean? — Default: false
???

assemble_denovo.filter_to_taxon.machine_mem_gb
Int? — Default: None
???

assemble_denovo.filter_to_taxon.neg_control_prefixes_space_separated
String? — Default: "neg water NTC"
???

assemble_denovo.filter_to_taxon.negative_control_reads_threshold
Int? — Default: 0
???

assemble_denovo.filter_to_taxon_db
File? — Default: None
Optional database to use to filter read set to those that match by LASTAL. Sequences in fasta format will be indexed on the fly.

assemble_denovo.isnvs_per_sample.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.10.0"
???

assemble_denovo.isnvs_per_sample.machine_mem_gb
Int? — Default: None
???

assemble_denovo.isnvs_per_sample.maxBias
Int? — Default: None
???

assemble_denovo.isnvs_per_sample.minReadsPerStrand
Int? — Default: None
???

assemble_denovo.isnvs_per_sample.removeDoublyMappedReads
Boolean — Default: true
???

assemble_denovo.isnvs_per_sample.sample_name
String — Default: basename(basename(basename(mapped_bam,".bam"),".all"),".mapped")
???

assemble_denovo.isnvs_per_sample.threads
Int? — Default: None
???

assemble_denovo.novocraft_license
File? — Default: None
???

assemble_denovo.nucmer_max_gap
Int? — Default: None
???

assemble_denovo.nucmer_min_cluster
Int? — Default: None
???

assemble_denovo.nucmer_min_match
Int? — Default: None
???

assemble_denovo.refine_2x_and_plot.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.1.10.0"
???

assemble_denovo.refine_2x_and_plot.machine_mem_gb
Int? — Default: None
???

assemble_denovo.refine_2x_and_plot.plot_coverage_novoalign_options
String? — Default: "-r Random -l 40 -g 40 -x 20 -t 100 -k"
???

assemble_denovo.refine_2x_and_plot.refine1_major_cutoff
Float? — Default: 0.5
???

assemble_denovo.refine_2x_and_plot.refine1_min_coverage
Int? — Default: 2
???

assemble_denovo.refine_2x_and_plot.refine1_novoalign_options
String? — Default: "-r Random -l 30 -g 40 -x 20 -t 502"
???

assemble_denovo.refine_2x_and_plot.refine2_major_cutoff
Float? — Default: 0.5
???

assemble_denovo.refine_2x_and_plot.refine2_min_coverage
Int? — Default: 3
???

assemble_denovo.refine_2x_and_plot.refine2_novoalign_options
String? — Default: "-r Random -l 40 -g 40 -x 20 -t 100"
???

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

assemble_denovo.rmdup_ubam.machine_mem_gb
Int? — Default: None
???

assemble_denovo.rmdup_ubam.method
String — Default: "mvicuna"
mvicuna or cdhit

assemble_denovo.scaffold.aligner
String? — Default: None
???

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

assemble_denovo.scaffold.machine_mem_gb
Int? — Default: None
???

assemble_denovo.scaffold.sample_name
String — Default: basename(basename(contigs_fasta,".fasta"),".assembly1-spades")
???

assemble_denovo.scaffold_min_length_fraction
Float? — Default: None
???

assemble_denovo.scaffold_min_pct_contig_aligned
Float? — Default: None
???

assemble_denovo.scaffold_min_unambig
Float? — Default: None
???

assemble_denovo.scaffold_replace_length
Int? — Default: 55
???

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