Scrub Jay Genomics

This is a minimal initial repository to track code for diploid assembly and long-read population genomics of scrub jays.

Where are the results?

Revelant output files can be found on the Cannon cluster at /n/holylfs05/LABS/informatics/Everyone/scrubjay/scrub-jay-genomics/workflow/results

Results subdirectories

REFERENCE ASSEMBLIES:

• HIC_REFERENCE_ASSEMS/AW_365336_FSJragtag.v1.fasta: scaffolded (HiC + Ragtag) A. woodhouseii reference female
• HIC_REFERENCE_ASSEMS/AW_365336_FSJragtag.v1.ALTLABEL.fasta: as above, but with headers in Panspec format (for PGGB)
• HIC_REFERENCE_ASSEMS/AW_365336_combined_repeats_v2.fasta: repeat library used for annotation (RepeatModeler + SRF)
• HIC_REFERENCE_ASSEMS/AW_365336_FSJragtag.v1.fasta.tbl: tabular output of RepeatMasker for reference individual
• HIC_REFERENCE_ASSEMS/AW_365336_FSJragtag.v1.fasta.out.gff: RepeatMasker annotation
• HIC_REFERENCE_ASSEMS/AW_365338_FSJragtag.v1.fasta: scaffolded reference for A. woodhouseii reference male

INDIVIDUAL ASSEMBLIES

• assemblies/*.p_ctg.fasta: unscaffolded primary assemblies
  • AC = A. coerulescens, Florida scrub jay
  • AI = A. insularis, Island scrub jay
  • AW = A. woodhouseii, Woodhouse scrub jay
  • CY = Yucatan scrub jay
• assemblies/*hap[1|2].p_ctg.fasta: unscaffolded haplotype assemblies
• assembly_qc/: basic assembly stats
• assembly_qc/ASSEMBLY_STATS.tsv: summary file of basic stats, primary and haplotype
• assembly_qc/READS_STATS.tsv: summary file with basic stats for FASTQ files used for each assembly

PANGENOME GRAPHS AND ANALYSIS

• NB: as of 2/1/23, several communities are still in process of construction
• PGGB/combined_assemblies.partition.paf: alignment file of all assembly haplotypes, plus reference and Yucatan jay
• PGGB/communities/: lists of all communities partitioned by wfmash
• PGGB/allbird_community.[0-9]: communities containing reference chromosomes
  • PGGB/allbird_community.[0-9]/*.paf: alignment file of sequences in community
  • PGGB/allbird_community.[0-9]/*.og: PGGB graph format of alignment (input to ODGI for visualization)
  • PGGB/allbird_community.[0-9]/*.gfa: standard graph format of alignment
  • PGGB/allbird_community.[0-9]/*.nameFix.vcf.gz: varaiant call format file deconstructed from .og file using vg deconstruct. Note: 'nameFix' version has the reference geneome ID as 'aphWoo1' to properly recolve haplotypes
  • PGGB/allbird_community.[0-9]/*final_nameFix_bub_wave.vcf: normalized and deconvoluted VCF file (run thru vcfwave and vcfbub). Use this file for pop gen analysis!
  • PGGB/allbird_community.[0-9]/*bub_wave_A[W|I|C]_bialle.vcf: normalized and deconvoluted VCF file of only biallelic SNPs, split by species
• PGGB/allbird_community.[0-9]_unplaced: communities containing unplaced reference scaffolds
  • Contains same files as above

SRF SATELLITES

• satellite/sj_sats_combined_assem.fa: KMC+SRF output with satellites from all combined (primary) assemblies
• satellite/sj_sats_vs_*/: combined satellites mapped against individual assemblies
  • sj_sats_srf-aln_vs_A[W|I|C]_*.bed: combined satellites mapped vs the individual genome
  • sj_sats_srf-aln_vs_A[W|I|C]_*_reads.bed: combined satellites mapped vs the individual genomic reads
    • There are also .paf (alignment) files and .len (repeat count summary) files for each sample
• results/satellite/individual_vs_reads/: KMC+SRF output from individual reads (i.e. NOT combined satellites)

GENE ANNOTATION

• gene_annotation/stringtie_RNAseq: annotation with Illumina, done using stringtie + hisat. BUSCO completeness 97%
  • scrubjay_stringtie_merge.gtf: merged GTF file from all samples
  • scrubjay_stringtie_transcripts.fa: transcripts extracted using gffread
• gene_annotation/IsoQuant/: annotation using PacBio Isoseq, done using IsoQuant. BUSCO completeness 88%
  • isoquant_merge.gtf: merged GTF file
  • transcripts.fa: transcripts extracted using gffread