mmlong2-dfs.md

Description of mmlong2 result dataframes

<output_name>_general.tsv

Category	Description
reads_n	Number of reads, reported by Nanoq
reads_yield_bp	Read yield, reported by Nanoq
reads_n50_bp	Read length N50 value, reported by Nanoq
reads_len_max_bp	Length of the longest read, reported by Nanoq
reads_len_min_bp	Length of the shortest read, reported by Nanoq
reads_mean_len_bp	Mean read length, reported by Nanoq
reads_median_len_bp	Median read length, reported by Nanoq
reads_mean_q	Mean read Phred quality score, reported by Nanoq
reads_median_q	Median read Phred quality score, reported by Nanoq
contigs_n	Number of assembled contigs, reported by Nanoq
contigs_yield_bp	Metagenome assembly size, reported by Nanoq
contigs_n50_bp	Contig length N50 value, reported by Nanoq
contigs_len_max_bp	Length of the longest contig, reported by Nanoq
contigs_len_min_bp	Length of the shortest contig, reported by Nanoq
contigs_mean_len_bp	Mean contig length, reported by Nanoq
contigs_median_len_bp	Median contig length, reported by Nanoq
mapped_identity_median	Mean read identity (%) to the assembled metagenome, reported by Cramino
mapped_identity_mean	Median read identity (%) to the assembled metagenome, reported by Cramino
contigs_circ	Number of circular contigs, reported by the assembler
all_bins	Total number of genome bins
circ_bins	Number of circular genome bins
hq_bins	Number of high-quality genome bins
mq_bins	Number of medium-quality genome bins
lq_bins	Number of low-quality genome bins
contaminated_bins	Number of contaminated genome bins
bin_cov_median	Median genome bin coverage
yield_assembled	Percentage of sequenced data assembled into contigs
yield_binned	Percentage of sequenced data that was binned
assembly_binned	Percent of assembly size that was binned
wf_name	Workflow output name
wf_mode	Workflow mode
wf_v	Workflow version
wf_date	Date of workflow completion

<output_name>_contigs.tsv

Category	Description
contig	Contig identifier
len_bp	Contig length
cov	Contig coverage, reported by the assembler
status_circular	Contig circularity status, reported by the assembler
tax_kaiju	Contig taxonomy, reported by Kaiju
tax_rrna	Contig taxonomy, based on 16S rRNA classification to a rRNA database
tophit_rrna	Percent identity for the best match in a rRNA database, reported by Vsearch
bin	Identifier for genome bin that contains the contig
gc	Contig guanine-cytosine content (%)
var_n	Number of detected nucleotide variants, reported by Longshot
var_perc	Percentage of contig with nucleotide variants
wf_name	Workflow output name
wf_mode	Workflow mode
wf_v	Workflow version
wf_date	Date of workflow completion

<output_name>_bins.tsv

Category	Description
bin	Genome bin identifier
completeness_checkm1	Genome bin completeness estimate, reported by CheckM
contamination_checkm1	Genome bin contamination estimate, reported by CheckM
strain_heterogeneity_checkm1	Genome bin strain heterogeneity index, reported by CheckM
completeness_checkm2	Genome bin completeness estimate, reported by CheckM2
contamination_checkm2	Genome bin contamination estimate, reported by CheckM2
coding_density	Genome bin gene coding density, reported by CheckM2
genome_size	Genome bin size (bp), reported by CheckM2
contigs	Number of contigs, reported by CheckM2
gc	Genome bin guanine-cytosine content (%), reported by Quast
contig_n50	Genome bin N50 (bp), reported by Quast
contig_n90	Genome bin N90 (bp), reported by Quast
aun	Nx area under the curve, reported by Quast
n_per_100kb	Rate of Ns in a genome bin per 100 kb, reported by Quast
cov	Genome bin coverage, reported by CoverM
r_abund	Genome bin relative abundance (%), reported by CoverM
bakta_cds_all	Number of protein coding genes, reported by Bakta
bakta_cds_hyp	Number of hypothetical protein coding genes, reported by Bakta
bakta_trna_all	Number of all tRNA genes genes, reported by Bakta
bakta_trna_uniq	Number of unique tRNA genes genes, reported by Bakta
bakta_16S	Number of 16S rRNA genes genes, reported by Bakta
bakta_23S	Number of 23S rRNA genes genes, reported by Bakta
bakta_5S	Number of 5S rRNA genes genes, reported by Bakta
barrnap_16S	Number of 16S rRNA genes genes, reported by Barrnap
barrnap_23S	Number of 23S rRNA genes genes, reported by Barrnap
barrnap_5S	Number of 5S rRNA genes genes, reported by Barrnap
custom_trna_uniq	Number of unique tRNA genes genes, reported by tRNAscan-SE
bin_status	Genome bin quality ranking according to MIMAG standards
cbin_status	Genome bin circularity status
gunc_css	Clade separation score, reported by GUNC
gunc_rrs	Reference representation score, reported by GUNC
gunc_pass	Chimerism test status, reported by GUNC
var_n	Number of detected nucleotide variants, reported by Longshot
var_perc	Percentage of genome bin with nucleotide variants
tax_gtdb	Genome bin taxonomy, reported by GTDB-tk
ref_gtdb	Reference for the closest genome bin match, reported by GTDB-tk
ani_gtdb	Average nucleotide identity for the closest match, reported by GTDB-tk
af_gtdb	Alignment fraction for the closest match, reported by GTDB-tk
msa_gtdb	Percentage of the multi-sequence alignment spanned by the genome bin, reported by GTDB-tk
red_gtdb	Genome bin relative evolutionary divergence, reported by GTDB-tk
warning_gtdb	Warning message, reported by GTDB-tk
tax_rrna	Genome bin taxonomy, based on 16S rRNA classification to a rRNA database
tophit_rrna	Percent identity for the best match in a rRNA database, reported by Vsearch
wf_name	Workflow output name
wf_mode	Workflow mode
wf_v	Workflow version
wf_date	Date of workflow completion