aligned_bai |
File |
Index companion file to the bam file generated during the consensus assembly process |
aligned_bam |
File |
Primer-trimmed BAM file; generated during conensus assembly process |
assembly_fasta |
File |
Consensus genome assembly |
assembly_length_unambiguous |
Int |
Number of unambiguous basecalls within the SC2 consensus assembly |
assembly_mean_coverage |
Float |
Mean sequencing depth throughout the conesnsus assembly generated after performing primer trimming–calculated using the SAMtools coverage command |
assembly_method |
String |
Method employed to generate consensus assembly |
auspice_json |
File |
Auspice-compatable JSON output generated from NextClade analysis that includes the NextClade default samples for clade-typing and the single sample placed on this tree |
bbduk_docker |
String |
Docker image used to run BBDuk |
bwa_version |
String |
Version of BWA used to map read data to the reference genome |
consensus_flagstat |
File |
Output from the SAMtools flagstat command to assess quality of the alignment file (BAM) |
consensus_stats |
File |
Output from the SAMtools stats command to assess quality of the alignment file (BAM) |
dehosted_read1 |
File |
Dehosted forward reads; suggested read file for SRA submission |
dehosted_read2 |
File |
Dehosted reverse reads; suggested read file for SRA submission |
fastqc_clean_pairs |
String |
Number of paired reads after SeqyClean filtering as determined by FastQC |
fastqc_clean1 |
Int |
Number of forward reads after seqyclean filtering as determined by FastQC |
fastqc_clean2 |
Int |
Number of reverse reads after seqyclean filtering as determined by FastQC |
fastqc_raw_pairs |
String |
Number of paired reads identified in the input fastq files as determined by FastQC |
fastqc_raw1 |
Int |
Number of forward reads identified in the input fastq files as determined by FastQC |
fastqc_raw2 |
Int |
Number of reverse reads identified in the input fastq files as determined by FastQC |
fastqc_version |
String |
Version of the FastQC software used for read QC analysis |
ivar_tsv |
File |
Variant descriptor file generated by iVar variants |
ivar_variant_version |
String |
Version of iVar for running the iVar variants command |
ivar_version_consensus |
String |
Version of iVar for running the iVar consensus command |
ivar_version_primtrim |
String |
Version of iVar for running the iVar trim command |
kraken_human |
Float |
Percent of human read data detected using the Kraken2 software |
kraken_human_dehosted |
Float |
Percent of human read data detected using the Kraken2 software after host removal |
kraken_report |
File |
Full Kraken report |
kraken_report_dehosted |
File |
Full Kraken report after host removal |
kraken_sc2 |
Float |
Percent of SARS-CoV-2 read data detected using the Kraken2 software |
kraken_sc2_dehosted |
Float |
Percent of SARS-CoV-2 read data detected using the Kraken2 software after host removal |
kraken_version |
String |
Version of Kraken software used |
meanbaseq_trim |
Float |
Mean quality of the nucleotide basecalls aligned to the reference genome after primer trimming |
meanmapq_trim |
Float |
Mean quality of the mapped reads to the reference genome after primer trimming |
nextclade_aa_dels |
String |
Amino-acid deletions as detected by NextClade |
nextclade_aa_subs |
String |
Amino-acid substitutions as detected by NextClade |
nextclade_clade |
String |
NextClade clade designation |
nextclade_json |
File |
NexClade output in JSON file format |
nextclade_tsv |
File |
NextClade output in TSV file format |
nextclade_version |
String |
Version of NextClade software used |
number_Degenerate |
Int |
Number of degenerate basecalls within the consensus assembly |
number_N |
Int |
Number of fully ambiguous basecalls within the consensus assembly |
number_Total |
Int |
Total number of nucleotides within the consensus assembly |
pango_lineage |
String |
Pango lineage as detremined by Pangolin |
pango_lineage_report |
File |
Full Pango lineage report generated by Pangolin |
pangolin_conflicts |
String |
Number of lineage conflicts as deteremed by Pangolin |
pangolin_docker |
String |
Docker image used to run Pangolin |
pangolin_notes |
String |
Lineage notes as deteremined by Pangolin |
pangolin_version |
String |
Pangolin and PangoLEARN versions used |
percent_reference_coverage |
Float |
Percent coverage of the reference genome after performing primer trimming; calculated as assembly_length_unambiguous / length of reference genome (SC2: 29,903) x 100 |
primer_trimmed_read_percent |
Float |
Percent of read data with primers trimmed as deteremined by iVar trim |
read1_clean |
File |
Forward read file after quality trimming and adapter removal |
read2_clean |
File |
Reverse read file after quality trimming and adapter removal |
samtools_version |
String |
Version of SAMtools used to sort and index the alignment file |
samtools_version_consensus |
String |
Version of SAMtools used to create the pileup before running iVar consensus |
samtools_version_primtrim |
String |
Version of SAMtools used to create the pileup before running iVar trim |
samtools_version_stats |
String |
Version of SAMtools used to assess quality of read mapping |
seq_platform |
String |
Description of the sequencing methodology used to generate the input read data |
titan_illumina_pe_analysis_date |
String |
Date of analysis |
titan_illumina_pe_version |
String |
Version of the Public Health Viral Genomics (PHVG) repository used |
trimmomatic_version |
String |
Version of Trimmomatic used |
vadr_alerts_list |
File |
File containing all of the fatal alerts as determined by VADR |
vadr_docker |
String |
Docker image used to run VADR |
vadr_num_alerts |
String |
Number of fatal alerts as determined by VADR |