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[TheiaProk] Add Sequins read extraction/decontamination #1021

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115e67e
add host_decontaminate
xonq Mar 13, 2026
4f8503c
add read_decontaminate call
xonq Mar 13, 2026
dcee5d1
fix syntax
xonq Mar 13, 2026
e2c2f1b
propagate decontaminate workflow outputs
xonq Mar 15, 2026
6aa6c6a
add readqc decontamination
xonq Mar 15, 2026
16c5609
fix input name
xonq Mar 15, 2026
14d233a
update i/o
xonq Mar 15, 2026
5969089
stage mapping
xonq Mar 16, 2026
6eb5d5e
add coverage/depth by sequence calculations
xonq Mar 16, 2026
459d93c
fix variable naming
xonq Mar 16, 2026
97b6bab
propagate new read mapping statistics to theiaviral and change output…
xonq Mar 16, 2026
a52e0d9
update output names, expand docs, incorporate docs, output host_decon…
xonq Mar 16, 2026
0a2aacd
propagate decontaminate to illumina_pe workflows
xonq Mar 16, 2026
1627014
rename output
xonq Mar 16, 2026
168b72e
panel is incompatible with mapped outputs
xonq Mar 16, 2026
bdc8ce0
update io doc
xonq Mar 16, 2026
df3473e
contaminate -> contaminant
xonq Mar 16, 2026
3f21473
make percent coverage
xonq Mar 16, 2026
048246f
mitigate no coverage zerodivisionerror
xonq Mar 17, 2026
b3dc9c9
change name
xonq Mar 18, 2026
398021f
change name
xonq Mar 18, 2026
3276249
transition host_decontaminate to read_decontaminate
xonq Mar 18, 2026
f8f1dbf
finalize input changes
xonq Mar 18, 2026
f98d96f
add contaminant_percent_mapped_reads
xonq Mar 18, 2026
f592d74
add contaminant status check
xonq Mar 20, 2026
c4cbe86
sort status list
xonq Mar 20, 2026
b74e413
update io docs
xonq Mar 20, 2026
5364dfa
Merge remote-tracking branch 'origin/main' into kzm-sequins-dev
xonq Mar 20, 2026
b967390
update readmapping stats
xonq Mar 25, 2026
7910a46
update contaminant check
xonq Mar 25, 2026
3b96ed8
formatting
xonq Mar 25, 2026
8f02d3f
adequate null population for map
xonq Mar 25, 2026
9ea394d
update map designation
xonq Mar 25, 2026
59f764c
remove blank entry
xonq Mar 25, 2026
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15 changes: 14 additions & 1 deletion docs/assets/tables/all_inputs.tsv
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Expand Up @@ -994,8 +994,11 @@ gubbins nuc_subst_model String Nucleotide substitution model to use with Gubbins
gubbins tree_args String Quoted string of further arguments passed to tree building algorithm Optional Snippy_Tree general
gubbins tree_builder String Application to use for Gubbins tree building algorithm: "raxml", "raxmlng", "iqtree", "iqtree-fast", "fasttree", "hybrid" (fasttree is used for the first tree, and raxml is used for later iterations), "rapidnj" raxml Optional Snippy_Tree general
host_decontaminate complete_only Boolean Only download genomes labeled "complete" False Optional TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel general
host_decontaminate expected_sequences String Comma-delimited list of expected sequences that match the host FASTA headers Optional TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel general
host_decontaminate is_accession Boolean Inputted "host" is an accession False Optional TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel general
host_decontaminate is_genome Boolean Inputted "host" is an assembly FASTA False Optional TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel general
host_decontaminate min_expected_coverage Float Minimum coverage for expected sequences to be identified 0 Optional TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel general
host_decontaminate min_expected_depth Int Minimum depth for expected sequences to be identified 0 Optional TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel general
host_decontaminate minimap2_memory Int Amount of memory/RAM (in GB) to allocate to the task 32 Optional TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel runtime
host_decontaminate read2 File Internal component, do not modify Optional TheiaViral_ONT general
host_decontaminate refseq Boolean Only download RefSeq genomes True Optional TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel general
Expand Down Expand Up @@ -1961,7 +1964,7 @@ raw_check_reads memory Int Amount of memory/RAM (in GB) to allocate to the task
raw_check_reads workflow_series String Internal component, do not modify theiaviral Optional TheiaEuk_ONT general
read_mapping_stats cpu Int Number of CPUs to allocate to the task 2 Optional TheiaViral_Illumina_PE, TheiaViral_ONT runtime
read_mapping_stats disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional TheiaViral_Illumina_PE, TheiaViral_ONT runtime
read_mapping_stats docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/staphb/samtools:1.23 Optional TheiaViral_Illumina_PE, TheiaViral_ONT docker
read_mapping_stats docker String The Docker container to use for the task us-docker.pkg.dev/general-theiagen/theiagen/pysam:1.23 Optional TheiaViral_Illumina_PE, TheiaViral_ONT docker
read_mapping_stats memory Int Amount of memory/RAM (in GB) to allocate to the task 8 Optional TheiaViral_Illumina_PE, TheiaViral_ONT runtime
read_mapping_stats read2 File Internal component, do not modify Optional TheiaViral_ONT general
read_QC_trim adapters File File with adapter sequences to be removed Optional TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE general
Expand All @@ -1981,6 +1984,7 @@ read_QC_trim call_kraken Boolean Internal component, do not modify False Optiona
read_QC_trim call_midas Boolean True/False variable that determines if the MIDAS task should be called. False Optional TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE general
read_QC_trim call_midas Boolean Internal component, do not modify False Optional TheiaEuk_Illumina_PE general
read_QC_trim downsampling_coverage Float The desired coverage to sub-sample the reads to with RASUSA 150 Optional TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT general
read_QC_trim expected_contaminants String Comma-delimited list of expected contaminant sequences. These must match "read_decontaminate_fasta" sequence headers Optional TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE general
read_QC_trim fastp_args String Additional arguments to use with fastp --detect_adapter_for_pe -g -5 20 -3 20 Optional TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE general
read_QC_trim fastp_args String Additional arguments to use with fastp -g -5 20 -3 20 Optional TheiaCoV_Illumina_SE, TheiaProk_Illumina_SE general
read_QC_trim kraken_cpu Int Number of CPUs to allocate to the task 4 Optional TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE runtime
Expand All @@ -1997,6 +2001,8 @@ read_QC_trim metabuli_memory Int Amount of memory/RAM (in GB) to allocate to the
read_QC_trim metabuli_taxdump_path File Path to taxonkit-generated taxdump for Metabuli taxonomy parsing gs://theiagen-public-resources-rp/reference_data/databases/metabuli/ncbi_taxdump_20260211.tar.gz Optional TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT general
read_QC_trim midas_db File Internal component, do not modify gs://theiagen-public-resources-rp/reference_data/databases/midas/midas_db_v1.2.tar.gz Optional TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE general
read_QC_trim midas_db File The database used by the MIDAS task in .tar.gz format gs://theiagen-public-resources-rp/reference_data/databases/midas/midas_db_v1.2.tar.gz Optional TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE database
read_QC_trim min_contaminant_coverage Float Minimum coverage to identify a contaminant sequence 0 Optional TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE general
read_QC_trim min_contaminant_depth Int Minimum depth to identify a contaminant sequence 0 Optional TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE general
read_QC_trim min_length Int Internal component, do not modify 400 Optional TheiaEuk_ONT, TheiaProk_ONT general
read_QC_trim nanoq_cpu Int Number of CPUs to allocate to the task 2 Optional TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT runtime
read_QC_trim nanoq_disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT runtime
Expand Down Expand Up @@ -2031,6 +2037,8 @@ read_QC_trim rasusa_number_of_reads Int Internal component, do not modify Optio
read_QC_trim rasusa_number_of_reads Int Subsample to a specific number of reads Optional TheiaEuk_ONT, TheiaProk_ONT general
read_QC_trim rasusa_seed Int Internal component, do not modify Optional TheiaCoV_ONT general
read_QC_trim rasusa_seed Int Random seed to use Optional TheiaEuk_ONT, TheiaProk_ONT general
read_QC_trim read_decontaminate_fasta File FASTA of contaminat sequences to map and remove reads against Optional TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE general
read_QC_trim read_decontaminate_memory Int Amount of memory/RAM (in GB) to allocate to the task 32 Optional TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE runtime
read_QC_trim read_processing String The name of the tool to perform basic read processing; options: "trimmomatic" or "fastp" trimmomatic Optional TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE general
read_QC_trim read_qc String The tool used for quality control (QC) of reads. Options are "fastq_scan" (default) and "fastqc" fastq_scan Optional TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE general
read_QC_trim run_prefix String Internal component, do not modify artic_ncov2019 Optional TheiaEuk_ONT, TheiaProk_ONT general
Expand Down Expand Up @@ -2081,13 +2089,18 @@ read_QC_trim_pe bbduk_memory Int Amount of memory/RAM (in GB) to allocate to the
read_QC_trim_pe bracken_kmer_length Int Kmer length for Bracken to use instead of auto-detection - must be present in database Optional Freyja_FASTQ general
read_QC_trim_pe call_bracken Boolean Call Bracken kraken2 report refinement False Optional Freyja_FASTQ general
read_QC_trim_pe call_midas Boolean True/False variable that determines if the MIDAS task should be called. False Optional Freyja_FASTQ general
read_QC_trim_pe expected_contaminants String Internal component, do not modify Optional Freyja_FASTQ general
read_QC_trim_pe fastp_args String Additional arguments to use with fastp --detect_adapter_for_pe -g -5 20 -3 20 Optional Freyja_FASTQ general
read_QC_trim_pe kraken_cpu Int Number of CPUs to allocate to the task 4 Optional Freyja_FASTQ runtime
read_QC_trim_pe kraken_db File A kraken2 database to use with the kraken2 optional task. The file must be a .tar.gz kraken2 database. gs://theiagen-public-resources-rp/reference_data/databases/kraken2/k2_viral-refseq_human-GRCh38_20260220.tar.gz Optional Freyja_FASTQ database
read_QC_trim_pe kraken_disk_size Int Amount of storage (in GB) to allocate to the task 100 Optional Freyja_FASTQ runtime
read_QC_trim_pe kraken_memory Int Amount of memory/RAM (in GB) to allocate to the task 32 Optional Freyja_FASTQ runtime
read_QC_trim_pe midas_db File Database to use with MIDAS. Not required as one will be auto-selected when running the MIDAS task. gs://theiagen-public-resources-rp/reference_data/databases/midas/midas_db_v1.2.tar.gz Optional Freyja_FASTQ database
read_QC_trim_pe min_contaminant_coverage Float Internal component, do not modify 0 Optional Freyja_FASTQ general
read_QC_trim_pe min_contaminant_depth Int Internal component, do not modify 0 Optional Freyja_FASTQ general
read_QC_trim_pe phix File The file containing the phix sequence to be used during bbduk task Optional Freyja_FASTQ general
read_QC_trim_pe read_decontaminate_fasta File FASTA of contaminat sequences to map and remove reads against Optional Freyja_FASTQ general
read_QC_trim_pe read_decontaminate_memory Int Amount of memory/RAM (in GB) to allocate to the task 32 Optional Freyja_FASTQ runtime
read_QC_trim_pe read_processing String Options: "trimmomatic" or "fastp" to indicate which read trimming module to use trimmomatic Optional Freyja_FASTQ general
read_QC_trim_pe read_qc String Allows the user to decide between fastq_scan (default) and fastqc for the evaluation of read quality. fastq_scan Optional Freyja_FASTQ general
read_QC_trim_pe trim_quality_min_score Int The minimum quality score to keep during trimming 30 Optional Freyja_FASTQ general
Expand Down
18 changes: 16 additions & 2 deletions docs/assets/tables/all_outputs.tsv
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Expand Up @@ -252,6 +252,17 @@ consensus_qc_number_N Int Number of N bases in consensus assembly TheiaViral_Ill
consensus_qc_number_Total Int Total number of bases in consensus assembly TheiaViral_Illumina_PE, TheiaViral_ONT
consensus_qc_percent_reference_coverage Float Percent of reference genome covered in consensus assembly TheiaViral_Illumina_PE, TheiaViral_ONT
consensus_stats File Output from the SAMtools stats command to assess quality of the alignment file (BAM) TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT
contaminant_bai File Index of reads aligned to the contaminant FASTA TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
contaminant_bam File Reads aligned to the contaminant FASTA TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
contaminant_cov_hist File Coverage histogram of reads mapped to contaminant FASTA TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
contaminant_coverage Float Mean coverage of reads mapped to contaminant FASTA TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
contaminant_coverage_by_sequence Map[String,Float] A JSON map relating sequence headers to read mapping coverage TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
contaminant_depth_by_sequence Map[String,Float] A JSON map relating sequence headers to read mapping depth TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
contaminant_mapping_flagstat File Samtools flagstat of reads mapped to contaminant FASTA TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
contaminant_mapping_stats File Samtools statistics of reads mapped to contaminant FASTA TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
contaminant_mean_depth Float Mean depth of reads mapped to contaminant FASTA TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
contaminant_percent_mapped_reads Float Percent of reads mapped to contaminant FASTA TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
contaminant_status String Status of contaminant sequence identification within sample TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
contig_number Int The number of contigs in the assembly_fasta (see description for `assembly_fasta`) TheiaMeta_Illumina_PE
contigs_gfa File Assembly graph output generated by SPAdes (Illumina: PE, SE) or Flye (ONT), used to visualize and evaluate genome assembly results. TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
cophylogeny_plot File A cophylogeny plot depicting branching order differences between two phylogenies without branch lengths PhyloCompare
Expand All @@ -267,16 +278,18 @@ datatable File Sample-level data table TSV file that was used to update the orig
dehost_wf_dehost_read1 File Reads that did not map to host TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_dehost_read2 File Paired-reads that did not map to host TheiaViral_Illumina_PE, TheiaViral_Panel
dehost_wf_host_accession String Host genome accession TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_coverage_by_sequence Map[String,Float] A JSON mapping relating host sequence headers to read mapping coverage TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_depth_by_sequence Map[String,Float] A JSON mapping relating host sequence headers to read mapping depth TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_fasta File Host genome FASTA file TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_flagstat File Output from the SAMtools flagstat command to assess quality of the alignment file (BAM) TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_mapped_bai File Indexed bam file of the reads aligned to the host reference TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_mapped_bam File Sorted BAM file containing the alignments of reads to the host reference genome TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_mapping_cov_hist File Coverage histogram from host read mapping TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_mapping_coverage Float Average coverage from host read mapping TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_mapping_mean_depth Float Average depth from host read mapping TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_mapping_metrics File File of mapping metrics TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_mapping_stats File File of mapping statistics TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_percent_mapped_reads Float Percentage of reads mapped to host reference genome TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dehost_wf_host_sequence_check String Status of host sequence identification in sample TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel
dnaapler_version String Version of dnaapler used TheiaEuk_ONT, TheiaProk_ONT
dorado_basecall_docker String Docker image used in the `dorado_basecall` task Dorado_Basecalling
dorado_basecall_version String Version of Dorado used in the `dorado_basecall` task Dorado_Basecalling
Expand Down Expand Up @@ -944,13 +957,14 @@ read2_unmapped File The unmapped reverse reads to the assembly TheiaMeta_Illumin
read_mapping_cov_hist File Coverage histogram from read mapping TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_cov_stats File Coverage statistics from read mapping TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_coverage Float Average coverage from read mapping TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_coverage_by_sequence Map[String,Float] A JSON map relating reference sequence headers to read mapping coverage TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_date String Date of read mapping analysis TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_depth Float Average depth from read mapping TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_depth_by_sequence Map[String,Float] A JSON map relating reference sequence headers to read mapping depth TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_flagstat File Flagstat file from read mapping TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_meanbaseq Float Mean base quality from read mapping TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_meanmapq Float Mean mapping quality from read mapping TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_percentage_mapped_reads Float Percentage of clean reads that mapped to the reference genome TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_report File Report file from read mapping TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_samtools_version String Version of samtools used in read mapping TheiaViral_Illumina_PE, TheiaViral_ONT
read_mapping_statistics File Statistics file from read mapping TheiaViral_Illumina_PE, TheiaViral_ONT
read_screen_clean String PASS or FAIL result from clean read screening; FAIL accompanied by the reason(s) for failure TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT
Expand Down
10 changes: 10 additions & 0 deletions docs/common_text/mapping_stats_task.md
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@@ -0,0 +1,10 @@
??? task "`mapping_stats`: Mapping Statistics"
The `mapping_stats` task generates mapping statistics from a BAM file. It uses samtools to generate a summary of the mapping statistics, which includes coverage, depth, average base quality, average mapping quality, and other relevant metrics. These statistics are also reported on a per sequence basis.

!!! techdetails "`mapping_stats` Technical Details"
| | Links |
| --- | --- |
| Task | [task_assembly_metrics.wdl](https://github.com/theiagen/public_health_bioinformatics/blob/main/tasks/quality_control/basic_statistics/task_mapping_stats.wdl) |
| Software Source Code | [samtools on GitHub](https://github.com/samtools/samtools) |
| Software Documentation | [samtools](https://www.htslib.org/doc/samtools.html) |
| Original Publication(s) | [The Sequence Alignment/Map format and SAMtools](https://doi.org/10.1093/bioinformatics/btp352)<br>[Twelve Years of SAMtools and BCFtools](https://doi.org/10.1093/gigascience/giab008) |
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