MiGA workflow

MiGA Workflow

This is the general overview of the MiGA workflow:

For each step, performed analyses may include the use of external Software, and produce one or more result files (indexed in a hash). In most steps, different utilities from the Enveomics Collection are used in addition to the Software detailed below. Some files are mandatory to continue with the analysis (marked with req), some can be gzipped during or after the analysis (marked with gz), and some are directories (marked with dir).

List of individual steps

Dataset Results

Raw Reads

This step is never actually performed by MiGA, instead it serves as the entry point for raw reads input.

Supported file keys:

For single reads only
- single (req, gz): FastQ file containing the raw reads
For paired-end reads only
- pair1 (req, gz): FastQ file containing the raw forward reads
- pair2 (req, gz): FastQ file containing the raw reverse reads

Statistics:

For single reads only
- reads: Total number of reads
- length_average: Average read length (in bp)
- length_standard_deviation: Standard deviation of read length (in bp)
- g_c_content: G+C content of all reads (in %)
- x_content: Undetermined bases content of all reads (in %)
- a_t_skew: A-T sequence skew across all reads (in %)
- g_c_skew: G-C sequence skew across all reads (in %)
For paired-end reads only
- read_pairs: Total number of read pairs
- forward_length_average: Average forward read length (in bp)
- forward_length_standard_deviation: Standard deviation of forward read
  length (in bp)
- forward_g_c_content: G+C content of forward reads (in %)
- forward_x_content: Undetermined bases content of forward reads (in %)
- forward_a_t_skew: A-T sequence skew across forward reads (in %)
- forward_g_c_skew: G-C sequence skew across forward reads (in %)
- reverse_length_average, reverse_length_standard_deviation,
- reverse_g_c_content: Same as above, for reverse reads
- reverse_x_content: Undetermined bases content of reverse reads (in %)
- reverse_a_t_skew: A-T sequence skew across reverse reads (in %)
- reverse_g_c_skew: G-C sequence skew across reverse reads (in %)

MiGA symbol: raw_reads.

Trimmed Reads

This is part of Trimming & read quality in the above diagram. In this step, MiGA trims reads by Phred quality score 20 (Q20) and minimum length of 50bp using SolexaQA++, and clips potential adapter contamination using Scythe (reapplying the length filter). If the reads are paired, only pairs passing the filters are used.

Supported file keys:

For single reads only
- single (req, gz): FastQ file containing trimmed/clipped reads
For paired-end reads only
- pair1 (req, gz): FastQ file containing trimmed/clipped forward reads
- pair2 (req, gz): FastQ file containing trimmed/clipped reverse reads
- single (req, gz): FastQ file containing trimmed/clipped reads with
  only one sister passing quality control
For either type
- trimming_summary: Raw text file containing a summary of the trimmed
  sequences

MiGA symbol: trimmed_reads.

Read Quality

This is a quality-control step included as part of Trimming & read quality in the diagram above. In this step, MiGA generates quality reports of the trimmed/clipped reads using SolexaQA++ and FastQC.

Supported file keys:

solexaqa (dir): Folder containing the SolexaQA++ quality-control
summaries
fastqc (dir): Folder containing the FastQC quality-control analyses

MiGA symbol: read_quality.

Trimmed FastA

This is the final step included in Trimming & read quality in the diagram above, in which MiGA generates FastA files with the trimmed/clipped reads.

Supported file keys:

coupled (req for coupled reads, unless pair1 and pair2 exist):
Interposed FastA file containing quality-checked paired reads. If this file
doesn't exist, it is automatically generated from pair1 and pair2
single (req for single reads, gz for coupled reads): FastA file with
quality-checked single-end reads
pair1 (gz): FastA file containing forward sisters of quality-checked
paired-end reads
pair2 (gz): FastA file containing reverse sisters of quality-checked
paired-end reads

Statistics:

reads: Total number of reads
length_average: Average read length (in bp)
length_standard_deviation: Standard deviation of read length (in bp)
g_c_content: G+C content of all reads (in %)
x_content: Undetermined bases content of all reads (in %)
a_t_skew: A-T sequence skew across all reads (in %)
g_c_skew: G-C sequence skew across all reads (in %)

MiGA symbol: trimmed_fasta.

Assembly

In this step MiGA assembles trimmed FastA reads using IDBA-UD.

Supported file keys:

largecontigs (req): FastA file containing large contigs or scaffolds
(>1Kbp)
allcontigs: FastA file containing all contigs or scaffolds (including
large)
assembly_data (dir): Folder containing some intermediate files generated
during the assembly

Statistics:

contigs: Total number of (large) contigs
n50: N50 of (large) contigs (in bp)
total_length: Total length of large contigs (in bp)
longest_sequence: Length of the longest contig (in bp)
n_content: Undetermined bases content of large contigs (in %)
g_c_content: G+C content of large contigs (in %)
x_content: Undetermined bases content of large contigs (in %)
a_t_skew: A-T sequence skew across large contigs (in %)
g_c_skew: G-C sequence skew across large contigs (in %)

MiGA symbol: assembly.

CDS

This step corresponds to Gene prediction in the diagram above. MiGA predicts coding sequences (putative genes and proteins) using Prodigal.

Supported file keys:

proteins (req): FastA file containing translated protein sequences
genes: FastA file containing putative gene sequences
gff3 (gz): GFF v3 file containing the coordinates of coding sequences
This file is not required, but MyTaxa depends on it (or gff2 or
tab, whichever is available)
gff2 (gz): GFF v2 file containing the coordinates of coding sequences
This file is not produced by MiGA, but it's supported for backwards
compatibility with earlier versions using MetaGeneMark
tab (gz): Tabular-delimited file containing the columns: gene ID, gene
length, and contig ID. This file is not produced by MiGA, but it's supported
to allow MyTaxa to run when more detailed information about the
gene prediction is missing

Statistics:

predicted_proteins: Total number of predicted proteins
average_length: Average length of predicted proteins (in aa)
coding_density: Coding density of the genome (in %)
codon_table: Optimal coding table (4 or 11)

MiGA symbol: cds.

Essential Genes

In this step, MiGA uses HMM.essential.rb from the Enveomics Collection to identify a set of genes typically present in single-copy in Bacterial and Archaeal genomes. In this step, protein translations of those essential genes are extracted for other analyses in MiGA (e.g., hAAI in distances) or outside (e.g., phylogeny or MLSA for diversity analyses). In addition, this step generates a report that can be used for quality control including estimations of completeness and contamination (for genomes) and median number of copies of single-copy genes (for metagenomes and viromes).

Supported file keys:

ess_genes (req): FastA file containing all extracted protein translations
from essential genes (.faa) or archived collection (proteins.tar.gz)
collection (req): Folder containing individual FastA files with protein
translations from essential genes
report (req): Raw text report including derived statistics, as well as
essential genes missing or detected in multiple copies (for genomes) or
copy counts (for metagenomes and viromes)
alignments: Generated for all genomes (non-multi types). It contains the
best matching protein for each detected model aligned to the model
bac_report: If present, this is the original report, and it indicates that a
corrected report has been generated to accomodate particular features of the
dataset

Statistics:

For metagenomes and viromes
- mean_copies: Average copy number across essential genes
- median_copies: Median copy number across essential genes
For genomes
- completeness: Estimated completeness of the genome, based on presence of
  essential genes (in %)
- contamination: Estimated contamination of the genome, based on copy number
  of essential genes (in %)
- quality: Completeness - 5 x Contamination

MiGA symbol: essential_genes.

SSU

In this step, MiGA detects small-subunit rRNA genes (16S) using Barrnap and extracts their sequences using Bedtools.

Supported file keys:

longest_ssu_gene (req): FastA file containing the longest detected SSU
gene
gff (gz): GFF v3 file containing the location of detected SSU genes
all_ssu_genes (gz): FastA file containing all the detected SSU genes

Statistics:

ssu: Total number of detected SSU fragments
complete_ssu: Number of complete SSU loci
max_length: Length of the longest detected SSU fragment

MiGA symbol: ssu.

MyTaxa

This step is only supported for metagenomes and viromes, and it requires the (optional) MyTaxa requirements installed.

In this step, the most likely taxonomic classification of each contig is identified using MyTaxa, and a report is generated using Krona.

Supported file keys:

mytaxa (req): Output generated by MyTaxa
blast (gz): BLAST against the reference genomes database
mytaxain (gz): Re-formatted BLAST used as input for MyTaxa
nomytaxa: If it exists, MiGA assumes no support for MyTaxa modules, and none
of the above files are required
species: Profile of species composition (in permil) as raw tab-delimited
text
genus: Profile of genus composition (in permil) as raw tab-delimited text
phylum: Profile of phylum composition (in permil) as raw tab-delimited text
innominate: List of innominate taxa (groups without a name but containing
lower-rank classifications) as raw text
kronain: Raw-text list of taxa used as input for Krona
krona: HTML output produced by Krona

MiGA symbol: mytaxa.

MyTaxa Scan

This step is only supported for genomes (dataset types genome, popgenome, and scgenome), and it requires the (optional) MyTaxa requirements installed.

In this step, the genomes are scanned in windows of ten genes. For each window, the taxonomic distribution is determined using MyTaxa and compared against the distribution for the entire genome. This is a quality-control step for manual curation.

Supported file keys:

mytaxa (req): MyTaxa output
report (req): PDF file containing the graphic report
regions_archive (gz): Archived folder containing FastA files with the
sequences of the genes in regions identified as abnormal
nomytaxa: If it exists, MiGA assumes no support for MyTaxa modules, and none
of the above files are required

Deprecated file keys:

wintax: Taxonomic distribution of each window
blast (gz): BLAST against the reference genomes database
mytaxain (gz): Re-formatted BLAST used as input for MyTaxa
regions (dir): Folder containing FastA files with the sequences of the
genes in regions identified as abnormal
gene_ids: List of genes per window
region_ids: List of regions identified as abnormal

MiGA symbol: mytaxa_scan.

Distances

This step is only supported for genomes (dataset types genome, popgenome, and scgenome). In this step, each dataset is compared against all other datasets in the project. If the dataset is a reference dataset, it is compared against all other reference datasets in the project. If it's a query dataset, it is compared iteratively against medoids. For more details on the strategy used in this step, see the manual section on distances.

Supported file keys:

For reference datasets
- haai_db (req): SQLite3 database containing hAAI values
- aai_db: SQLite3 database containing AAI values
- ani_db: SQLite3 database containing ANI values
For query datasets
- aai_medoids (req except for clades projects): Best hits among medoids
  at different hierarchical levels in the AAI indexing
- ani_medoids (req for clades projects): Best hits among medoids at
  different hierarchical levels in the ANI indexing
- haai_db (req): SQLite3 database containing hAAI values
- aai_db: SQLite3 database containing AAI values
- ani_db: SQLite3 database containing ANI values
- ref_tree: Newick file with the Bio-NJ tree including queried medoids and
  the query dataset
- ref_tree_pdf: PDF rendering of ref_tree
- intax: Raw text result of the taxonomy test against the reference genome

MiGA symbol: distances.

Taxonomy

This step is only supported for genomes (dataset types genome, popgenome, and scgenome) that are reference datasets, in projects with a set reference project (:ref_project in metadata).

In this step, MiGA compares the genome against a reference project using the query search method, and imports the resulting taxonomy with p-value below 0.05 (or whichever value is set as :tax_pvalue in metadata).

Supported file keys:

intax: Raw text result of the taxonomy test against the reference genome
aai_medoids (req except for reference clades projects): Best hits among
medoids at different hierarchical levels in the AAI indexing
ani_medoids (req for reference clades projects): Best hits among medoids
at different hierarchical levels in the ANI indexing
haai_db (req): SQLite3 database containing hAAI values
aai_db: SQLite3 database containing AAI values
ani_db: SQLite3 database containing ANI values
ref_tree: Newick file with the Bio-NJ tree including queried medoids and
the query dataset
ref_tree_pdf: PDF rendering of ref_tree

Statistics:

closest_relative: Name of the reference dataset with highest AAI
aai: AAI to the closest relative
domain_pvalue, phylum_pvalue, class_pvalue, order_pvalue,
family_pvalue, genus_pvalue, species_pvalue, subspecies_pvalue:
Empirical p-values for classification at each rank with respect to the closest
relative, based on the observed AAI

MiGA symbol: taxonomy

Stats

In this step, MiGA traces back all the results of the dataset and estimates summary statistics. In addition, it cleans any stored values in the distances database including datasets no longer registered in the project.

No supported file keys.

MiGA symbol: stats.

Project Results

Once all datasets have been pre-processed (i.e., once all the results above are available for all reference datasets), MiGA executes the following project-wide steps:

hAAI Distances

Consolidation of hAAI distances.

Supported file keys:

rdata (req): Pairwise values in a data.frame for R
matrix (req): Pairwise values in a raw tab-delimited file
log (req): List of datasets included in the matrix
hist: Histogram of hAAI values as raw tab-delimited file

MiGA symbol: haai_distances.

AAI Distances

Consolidation of AAI distances.

Supported file keys:

rdata (req): Pairwise values in a data.frame for R
matrix (req): Pairwise values in a raw tab-delimited file
log (req): List of datasets included in the matrix
hist: Histogram of AAI values as raw tab-delimited file

MiGA symbol: aai_distances.

ANI Distances

Consolidation of ANI distances.

Supported file keys:

rdata (req): Pairwise values in a data.frame for R
matrix (req): Pairwise values in a raw tab-delimited file
log (req): List of datasets included in the matrix
hist: Histogram of ANI values as raw tab-delimited file

MiGA symbol: ani_distances.

Clade Finding

This step is only supported for project types genomes and clade.

In this step, MiGA attempts to identify clades at species level or above using a combination of ANI and AAI values. MiGA generates AAI clades in this step for genomes projects. Clades proposed at AAI > 90% and ANI > 95% are formed using the Markov Clustering algorithm implemented in MCL. Most distance manipulation and tree estimation and manipulation utilities use the R packages Ape and Vegan.

Supported file keys:

report (req for genomes): PDF file including a graphic report for the
clustering
class_table (req for genomes): Tab-delimited file containing the
classification of all datasets in AAI clusters
class_tree (req for genomes): Newick file containing the classification
of all datasets in AAI clusters as a dendrogram
classif (req for genomes): Tab-delimited file containing the
highest-level classification of each dataset, the medoid of the cluster, and
the AAI against the corresponding medoid
medoids (req for genomes): List of medoids per cluster
aai_tree: Bio-NJ tree based on AAI distances in Newick format
proposal (req): Proposed species-level clades in the project, based on
clades_ani95. One line per proposed clade, with tab-delimited dataset names.
Only clades with 5 or more members are included
clades_aai90: Clades formed at AAI > 90%. One clade per line, with
comma-delimited dataset names
clades_ani95: Clades formed at ANI > 95%. One clade per line, with
comma-delimited dataset names
medoids_ani95: List of clades_ani95 datasets with the smallest ANI
distance to all members of its own ANI95 clade. The list is in the same order

MiGA symbol: clade_finding.

Subclades

This step is only supported for project type clade.

In this step, MiGA attempts to identify clades below species level using ANI values. MiGA generates ANI clades in this step. Most distance manipulation and tree estimation and manipulation utilities use the R packages Ape and Vegan.

Supported file keys:

report (req): PDF file including a graphic report for the clustering
class_table (req): Tab-delimited file containing the classification of all
datasets in ANI clusters
class_tree (req): Newick file containing the classification of all
datasets in ANI clusters as a dendrogram
classif (req): Tab-delimited file containing the highest-level
classification of each dataset, the medoid of the cluster, and
the ANI against the corresponding medoid
medoids (req): List of medoids per cluster
ani_tree: Bio-NJ tree based on AAI distances in Newick format

MiGA symbol: subclades.

OGS

This step is only supported for project type clade.

In this step, MiGA generates groups of orthology using reciprocal best matches between all pairs of datasets in the project. Groups are generated using MCL with pairs weighted by bit score. Once computed, MiGA uses the matrix of OGS to estimate summary and rarefied statistics.

Supported file keys:

ogs (req): Matrix of orthology groups, as tab-delimited raw file
stats (req): Summary statistics in JSON format
abc (gz): When available, it includes all the individual RBM files in
ABC format. This file is typically produced as intermediate result and
removed before finishing, but can be maintained using
miga update -P . -m clean_ogs=false in the project folder using the
CLI
core_pan: Summary statistics of rarefied core-genome/pangenome sizes in
tab-delimited format
core_pan_plot: Plot of rarefied core-genome/pangenome sizes in PDF

MiGA symbol: ogs.

Project Stats

In this step, MiGA traces back all the results of the project and estimates summary statistics.

Supported file keys:

taxonomy_index (req): Index of datasets per taxonomy in JSON format
metadata_index (req): Searchable index of datasets metadata as SQLite3
database

MiGA symbol: project_stats.

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