To the extent possible under law,
the person who associated CC0
with this work has waived all copyright and related or neighboring
rights to this work.
The read data for this analysis is in SRA under accession number PRJNA340324
Expect read-1 and read-2 fastq files for each of the following libraries. FIle paths in notebooks my need to be adjusted depending on where you place the files on your machine (big data is usually placed outsied the work drive and the path for those are system specific)
| Sample | Library | Used in analysis |
|---|---|---|
| MincA14 | 150715_D00248_0103_AC75KUANXX_4_IL-TP-021 | + |
| MareHarA | 150403_D00261_0236_AC6E37ANXX_8_IL-TP-021 | + |
| MareHarA | 150403_D00261_0236_AC6E37ANXX_8_IL-TP-023 | |
| MareHarA | 150521_D00200_0260_AC6V40ANXX_2_IL-TP-021 | |
| MareHarA | 150521_D00200_0260_AC6V40ANXX_2_IL-TP-023 | |
| MjavLD15 | 150715_D00248_0103_AC75KUANXX_4_IL-TP-010 | + |
| MincL19 | 150715_D00248_0103_AC75KUANXX_4_IL-TP-011 | + |
| MareL32 | 150715_D00248_0103_AC75KUANXX_4_IL-TP-022 | + |
| MareL28 | 150715_D00248_0103_AC75KUANXX_4_IL-TP-008 | + |
| MjavL57 | 150715_D00248_0103_AC75KUANXX_4_IL-TP-001 | + |
| MjavVW4 | mjavanicaVW4_500 | + |
| MjavVW4 | mjavanicaVW4_300 | |
| MincW1 | 150212_D00261_0225_AC6EKCANXX_1_IL-TP-013 | + |
| MincW1 | 150212_D00261_0225_AC6EKCANXX_1_IL-TP-005 | |
| MincVW6 | 150212_D00261_0225_AC6EKCANXX_1_IL-TP-007 | + |
| MincVW6 | 150212_D00261_0225_AC6EKCANXX_1_IL-TP-002 | |
| MincHarC | 150212_D00261_0225_AC6EKCANXX_1_IL-TP-012 | + |
| MincHarC | 150212_D00261_0225_AC6EKCANXX_1_IL-TP-004 | |
| Minc557R | 150212_D00261_0225_AC6EKCANXX_1_IL-TP-006 | + |
| MincL9 | 150715_D00248_0103_AC75KUANXX_4_IL-TP-009 | + |
| MincL27 | 150715_D00248_0103_AC75KUANXX_4_IL-TP-020 | + |
| MjavLD17 | 150715_D00248_0103_AC75KUANXX_4_IL-TP-003 | + |
| MentL30 | 150716_D00248_0104_BC75KYANXX_3_IL-TP-005 | + |
| MentL30 | 150716_D00248_0104_BC75KYANXX_3_IL-TP-019 | |
| MfloSJF1 | 160425_E00397_0014_AHLYG7CCXX_1_TP-D7-003 | + |
| MfloSJF1 | 160426_K00166_0058_AH7WLVBBXX_8_TP-D7-005_TP-D5-003 |
Genome assembly scripts by Dr. Laura Salazar are available here. The genome assembly files are in this repository.
These were used for mapping of genes and of contig pairs, based on raw read libraries indicated by + . They are available in this location until 25/6/2018. Aternatively, they can be created in notebook 2.
These were used for mitochondrial genome assembly, based on the first read trimmed file. When link is provided instead of a file, the trimmed read one file had less than 25 M reads in it and was also used as the subset. The links will need to be recreated on your system. These files are created in notebook 5.
Notebook file name: Dependencies.ipynb
Notebook file name: CDSs_and_proteins_from_genome_assemblies.ipynb
meloidogyne_assemblies: contains fasta genome assemblies
annotation: contain gff files for the assemblies in assemblies
<None | stopped | all>_<gene | cds | protein>_ref_<files | centroids | reviewed>
with None indicating that nothing is written.
- dirs that start with
None: genes, cdss or proteins without premature stop codon - dirs that start with
stopped: genes, cdss or proteins with a premature stop codon - dirs that start with
all: a merge ofNoneandstopped - dirs that end with
files: raw, as indicated in the gff - dirs that end with
centroinds: cds files that were reduced with a vsearch step - dirs that end with
reviewed: final treated datasets (see notebook) refin all the dir names indicate that these files are derived from a genome assembly annotation.
Notebook file name: Map_assemble_gene.ipynb
<sample name>_bwa/<sample name>.nt.fasta: map-assembled gene files
<None | stopped | all >_<cdss | proteins | gffs>
with None indicating that nothing is written.
- dirs that start with
None: gffs, cdss or proteins without premature stop codon - dirs that start with
stopped: gffs, cdss or proteins with a premature stop codon - dirs that start with
all: a merge ofNoneandstopped
Notebook file name: Orthology_clustering.ipynb
orthofinder/all_inputs/<sample name><None|_ref>.aa.fasta: links to protein sequences of all the samples. They will need to be regenerated locally (step included in the notebook).
orthofinder/all_inputs/Results_Jan16/<inflation value>_OrthologousGroup.csv: Orthology clusters, with <inflation value> representign the mcl inflation parameter, except for 0, representing an inflation of 1.5, and 1, representing inflation of 1.1.
orthofinder/all_inputs/Results_Jan16/WorkingDirectory: OrthoFinder inputs and outputs of the Blast step.
orthofinder/all_inputs/Results_Jan16/OGs_I2_1-4.gb.gz: A genbank file with coding and protein sequences of orthology clusters with 1 to 4 gene copies for each reference sample`.
orthofinder/all_inputs/Results_Jan16/OGs_I2_1-4.gb.loci.<csv|txt>: ReproPhylo formated list of the loci that are in the genbank file.
orthofinder/all_inputs/Results_Jan16/rootknot_phylogenomics: Input and output files of the OC filtering and correction pipeline, with trimal settings of gt=0.7 and st=0.01`
orthofinder/all_inputs/Results_Jan16/I2_3X2_gt0.7_st_0.01_alns_<1-4 | all2 | flo2>: Sequence alignments of orthology clusters in which inparalogs are collapsed into a single sequence, OCs with fragmanted orthologs are excluded and each genome copy contains up to one copy per sample.
1-4: all the orthology clusters in which there are at least 3 reference samples with 2 gene copies.
all2: a subset of 1-4 in which all the reference samples have two gene copies.
flo2: a subset of 1-4 in which all MfloSJF1 has two gene copies.
Notebook file name: Nuclear_phylogenomics.ipynb
orthofinder/all_inputs/Results_Jul02/I2_3X2_gt0.7_st_0.01_alns_1-4/<astralshuffeled | raxmlshuffled>: randomization analyses in which homeolog 1 and homeolog 2 are randomly assigned for each gene.
astralshuffeled: 100 astral runs, in which hom 1 and 2 were randomly assigend for each gene.
raxmlshuffled: 100 raxml supermatrix trees, in which hom 1 and 2 were randomly assigned for each gene, prior to the concatenation of the supermatrix.
orthofinder/all_inputs/Results_Jul02/I2_3X2_gt0.7_st_0.01_alns_1-4/trees.txt: a list of gene trees that were used for astral (non randomized)
orthofinder/all_inputs/Results_Jul02/I2_3X2_gt0.7_st_0.01_alns_1-4/raxmlshuffled/trees.txt: a list of randomized supermatrix trees.
orthofinder/all_inputs/Results_Jul02/I2_3X2_gt0.7_st_0.01_alns_1-4/ RAxML_StrictConsensusTree<AstStrict | RaxStrict>: strict consensus trees that resulted from the two randomization analyses with astral and raxml.
orthofinder/all_inputs/Results_Jul02/I2_3X2_gt0.7_st_0.01_alns_1-4/ RAxML_<>.merged_clusters_<>:
A through raxml tree reconstrction of a supermatrix of all the OCs, following a treeCL analysis confirming their shared phylogeny.
Notebook file name: Mitochondrial_genome_assembly.ipynb
<sample name>_mitobim: mitobim assembly based on mitochondrial gene seeds.
mito_references: reference mitochondrial genomes from ncbi.
Notebook file name: Mitochondrial_genomes_annotation.ipynb
mitochondrial_assemblies/<sample name>_genes.fasta: fasta files of mitochondrial genes as predicted by exonerate.
Notebook file name: Mitochondrial_genomes_tree.ipynb
mitochondrial_assemblies/phylogenetic_analysis: all the files associated with the reprophylo pipeline.
Notebook file name: Intra_genome_sequence_divergence.ipynb
intrablast_p_ident_dict.pkl: pairwise homoeolog identity values for all the samples.
Notebook file name: Median_ratio.ipynb
<sample>_contig_pairs_bwa: read mapping to homoeolog contig pairs.
coverage_ratio_histograms: outputs.
genes_to_contigs.pkl: contig assignment of genes.
OG_contig_relationship.pkl: contig assignments of OCs.
contig_pairs_data: fasta files with contigs pairs.
Notebook file name: GeneConversion.ipynb
synteny: all the related files.
Notebook file name: TE.ipynb
TEs: all the related files.
Notebook file name: GeneticVariation.ipynb
