GitHub - dluecke/FlyComparativeGenomics

Working space for genome assembly tools.

See comments in individual scripts for details on purpose, inputs, requirements, etc.

Everything is written to run on the USDA Ceres cluster SLURM system.

Feel free to reach out with questions: David.Luecke@usda.gov

Name		Name	Last commit message	Last commit date
Latest commit History 705 Commits
configs		configs
nextflow_info		nextflow_info
AlignDivergedWindows.sh		AlignDivergedWindows.sh
GetPurgedBuscoContigs.sh		GetPurgedBuscoContigs.sh
MakeTissueDatabase.py		MakeTissueDatabase.py
PlotsForAssemblyCuration.R		PlotsForAssemblyCuration.R
PlotsForAssemblyCuration.slurm		PlotsForAssemblyCuration.slurm
PrepareCurationPlots.sh		PrepareCurationPlots.sh
README.md		README.md
RagTagShield-writeGFF.R		RagTagShield-writeGFF.R
ReciprocalBLAST.sh		ReciprocalBLAST.sh
Reciprocal_RagTag-NoReads.slurm		Reciprocal_RagTag-NoReads.slurm
Reciprocal_RagTag.sh		Reciprocal_RagTag.sh
Reciprocal_RagTag.slurm		Reciprocal_RagTag.slurm
Reciprocal_RagTag.smk		Reciprocal_RagTag.smk
RunFCS-VPGRU.sh		RunFCS-VPGRU.sh
RunGenomeScope-VPGRU.sh		RunGenomeScope-VPGRU.sh
RunJuicerPost.sh		RunJuicerPost.sh
RunMerylMerqury-VPGRU.sh		RunMerylMerqury-VPGRU.sh
RunMummerAlignment-VPGRU.sh		RunMummerAlignment-VPGRU.sh
RunPbmm2-VPGRU.sh		RunPbmm2-VPGRU.sh
RunPurgeDups-VPGRU.sh		RunPurgeDups-VPGRU.sh
RunYahs.sh		RunYahs.sh
SRA-prefetch_fasterqdump-EGAPx.slurm		SRA-prefetch_fasterqdump-EGAPx.slurm
SRA-prefetch_fasterqdump.slurm		SRA-prefetch_fasterqdump.slurm
SRA-prefetch_fastqdump.slurm		SRA-prefetch_fastqdump.slurm
SexSpecificScaffolds-FUNCTIONS.R		SexSpecificScaffolds-FUNCTIONS.R
VPGRU-FCS_screen_TEMPLATE.slurm		VPGRU-FCS_screen_TEMPLATE.slurm
VPGRU-JuicerPost_TEMPLATE.slurm		VPGRU-JuicerPost_TEMPLATE.slurm
VPGRU-KmerAnalysis_TEMPLATE.slurm		VPGRU-KmerAnalysis_TEMPLATE.slurm
VPGRU-MummerAlignment_TEMPLATE.slurm		VPGRU-MummerAlignment_TEMPLATE.slurm
VPGRU-PurgeDups_TEMPLATE.slurm		VPGRU-PurgeDups_TEMPLATE.slurm
VPGRU-YaHS_TEMPLATE.slurm		VPGRU-YaHS_TEMPLATE.slurm
VPGRU-meryl_merqury_TEMPLATE.slurm		VPGRU-meryl_merqury_TEMPLATE.slurm
VPGRU-order_chromosomes.slurm		VPGRU-order_chromosomes.slurm
VPGRU-pbmm2_TEMPLATE.slurm		VPGRU-pbmm2_TEMPLATE.slurm
VPGRU-write_breakpoint_fastas.slurm		VPGRU-write_breakpoint_fastas.slurm
alignment_region_dotplot-FUNCTIONS.R		alignment_region_dotplot-FUNCTIONS.R
bcfcall.slurm		bcfcall.slurm
bcftools_view-alts.slurm		bcftools_view-alts.slurm
bcftools_view-hets.slurm		bcftools_view-hets.slurm
blastn.slurm		blastn.slurm
busco5_arachnida.slurm		busco5_arachnida.slurm
busco5_arthropoda.slurm		busco5_arthropoda.slurm
busco5_diptera.slurm		busco5_diptera.slurm
busco5_endopterygota.slurm		busco5_endopterygota.slurm
busco5_hemiptera.slurm		busco5_hemiptera.slurm
busco5_hymenoptera.slurm		busco5_hymenoptera.slurm
busco5_insecta.slurm		busco5_insecta.slurm
busco6_diptera12.slurm		busco6_diptera12.slurm
bwa-hic.slurm		bwa-hic.slurm
bwa.slurm		bwa.slurm
collect_FCS_taxa_summaries.sh		collect_FCS_taxa_summaries.sh
combine_haps.sh		combine_haps.sh
extract_fastqc_stats.sh		extract_fastqc_stats.sh
fasta-HiFi.slurm		fasta-HiFi.slurm
fastq-HiFi.slurm		fastq-HiFi.slurm
fastqc.slurm		fastqc.slurm
get_depth_by_scaffold.sh		get_depth_by_scaffold.sh
get_depth_by_window.sh		get_depth_by_window.sh
get_nmasked_by_window.sh		get_nmasked_by_window.sh
get_pct_chrs.sh		get_pct_chrs.sh
get_reads_spanning_BLAST_hits.sh		get_reads_spanning_BLAST_hits.sh
get_spanning_reads.sh		get_spanning_reads.sh
get_uniquegenes_gff.sh		get_uniquegenes_gff.sh
get_variants_by_sequence.sh		get_variants_by_sequence.sh
get_variants_by_window.sh		get_variants_by_window.sh
gfastats.slurm		gfastats.slurm
hardmask.slurm		hardmask.slurm
hifiasm_dualscaf.slurm		hifiasm_dualscaf.slurm
hifiasm_simple.slurm		hifiasm_simple.slurm
minimap2-ONT.sh		minimap2-ONT.sh
mitohifi.slurm		mitohifi.slurm
muscle.slurm		muscle.slurm
order_chromosomes.sh		order_chromosomes.sh
otb.VPGRU.template.slurm		otb.VPGRU.template.slurm
paftools-bam2paf.slurm		paftools-bam2paf.slurm
paftools-sam2paf.slurm		paftools-sam2paf.slurm
plot_BUSCO_results-2025.py		plot_BUSCO_results-2025.py
plot_BUSCO_results-Calliphoridae.py		plot_BUSCO_results-Calliphoridae.py
plot_BUSCO_results-Dmel_muller.py		plot_BUSCO_results-Dmel_muller.py
plot_BUSCO_results-vs_Mdom.py		plot_BUSCO_results-vs_Mdom.py
plot_BUSCO_results.py		plot_BUSCO_results.py
ragtag.sh		ragtag.sh
ragtag_correct.sh		ragtag_correct.sh
ragtag_gff.sh		ragtag_gff.sh
ragtag_scaffold.sh		ragtag_scaffold.sh
ragtag_scaffold.slurm		ragtag_scaffold.slurm
recip_ragtag-copy_logs.sh		recip_ragtag-copy_logs.sh
recip_ragtag-link_results.sh		recip_ragtag-link_results.sh
redo_hic_contacts-NoSplit.slurm		redo_hic_contacts-NoSplit.slurm
redo_hic_contacts.slurm		redo_hic_contacts.slurm
repeatmasker-TMPDIR.slurm		repeatmasker-TMPDIR.slurm
repeatmodeler_repeatmasker-TMPDIR.slurm		repeatmodeler_repeatmasker-TMPDIR.slurm
repeatmodeler_repeatmasker.slurm		repeatmodeler_repeatmasker.slurm
rephase_XY-FUNCTIONS.R		rephase_XY-FUNCTIONS.R
samtools_bamstats.slurm		samtools_bamstats.slurm
samtools_coverage.slurm		samtools_coverage.slurm
samtools_depth.slurm		samtools_depth.slurm
samtools_view-q.slurm		samtools_view-q.slurm

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