Name		Name	Last commit message	Last commit date
perlmods		perlmods
.gitignore		.gitignore
CDS2seq.v2.pl		CDS2seq.v2.pl
DnadiffCircosParser.pl		DnadiffCircosParser.pl
FastaToTbl		FastaToTbl
Nseries.pl		Nseries.pl
README.md		README.md
TblToFasta		TblToFasta
agp2bed.pl		agp2bed.pl
agp2fasta.pl		agp2fasta.pl
assemble_r103_min_high_g345_dnadiff.sh		assemble_r103_min_high_g345_dnadiff.sh
assemble_r941_min_high_g344_dnadiff.sh		assemble_r941_min_high_g344_dnadiff.sh
assembly_manifest.pl		assembly_manifest.pl
assignIDs_generic_fast.pl		assignIDs_generic_fast.pl
change_coordinates_from_bedgraph.pl		change_coordinates_from_bedgraph.pl
change_coordinates_from_gff3.pl		change_coordinates_from_gff3.pl
check_file_compression.py		check_file_compression.py
choose_best_super.pl		choose_best_super.pl
choose_best_super.py		choose_best_super.py
cis_pairs_dist.v03.R		cis_pairs_dist.v03.R
cnag_pipeline.pl		cnag_pipeline.pl
cnag_submit.pl		cnag_submit.pl
cnag_submit_cluster2.pl		cnag_submit_cluster2.pl
coding_potential.pl		coding_potential.pl
coding_potential_track_faster.pl		coding_potential_track_faster.pl
compress_fast5.py		compress_fast5.py
compress_files.sh		compress_files.sh
conversion_utils.py		conversion_utils.py
copy_ont_gridion_runs.sh		copy_ont_gridion_runs.sh
copy_ont_runs.sh		copy_ont_runs.sh
copysubproject.sh		copysubproject.sh
cutesv2bed.pl		cutesv2bed.pl
decontaminate_assembly_v02.pl		decontaminate_assembly_v02.pl
dnadiff_to_QV.pl		dnadiff_to_QV.pl
dovetail2chain.pl		dovetail2chain.pl
ena_download.sh		ena_download.sh
eval_annotations.pl		eval_annotations.pl
eval_nextgeneid.pl		eval_nextgeneid.pl
exon2intronGFFflankseqScoreBDF2.pl		exon2intronGFFflankseqScoreBDF2.pl
exon2intron_TranscriptSorted_simple.pl		exon2intron_TranscriptSorted_simple.pl
fast5_subset.py		fast5_subset.py
fasta-stats.py		fasta-stats.py
fasta2agp.pl		fasta2agp.pl
fastalength		fastalength
fastq2fasta.pl		fastq2fasta.pl
filterONTminimap2.sh		filterONTminimap2.sh
filter_fasta_from_ids.pl		filter_fasta_from_ids.pl
filtering_idslist.pl		filtering_idslist.pl
filtering_protein_list.pl		filtering_protein_list.pl
filtering_scaffoldslist.pl		filtering_scaffoldslist.pl
filtering_transcriptlist.pl		filtering_transcriptlist.pl
fixagp.pl		fixagp.pl
fixchragp.pl		fixchragp.pl
format_assembly.pl		format_assembly.pl
gaps-analysis-FCR.pl		gaps-analysis-FCR.pl
gem2dist.pl		gem2dist.pl
genome_coverage_stats-i-buchhalter.pl		genome_coverage_stats-i-buchhalter.pl
get_closest_mitogenome.py		get_closest_mitogenome.py
gfa2fasta.pl		gfa2fasta.pl
gfa_summary.pl		gfa_summary.pl
gff2gb.pl		gff2gb.pl
gff_stats.JGG.pl		gff_stats.JGG.pl
gtf_to_gff2or3.pl		gtf_to_gff2or3.pl
hobrac.sh		hobrac.sh
indexGenome.pl		indexGenome.pl
initialize_assembly_dir_cwd.sh		initialize_assembly_dir_cwd.sh
initialize_curation_dir.sh		initialize_curation_dir.sh
initialize_project.sh		initialize_project.sh
join_agp.pl		join_agp.pl
lims.py		lims.py
limsq		limsq
link_illumina_per_sample.v05.pl		link_illumina_per_sample.v05.pl
link_ont_fastq_stats_per_sample.pl		link_ont_fastq_stats_per_sample.pl
link_ont_gridion_subproject.sh		link_ont_gridion_subproject.sh
link_ont_subproject.sh		link_ont_subproject.sh
lowcomplexity_filter.pl		lowcomplexity_filter.pl
make_dist.v4.pl		make_dist.v4.pl
makesubdirs.pl		makesubdirs.pl
mnsubmit		mnsubmit
multi_to_single_fast5.py		multi_to_single_fast5.py
ncChunkedUploader.bash		ncChunkedUploader.bash
pafbased_rename.py		pafbased_rename.py
phasedVCF2alleles.pl		phasedVCF2alleles.pl
plot_dist2.R		plot_dist2.R
plot_treemap.R		plot_treemap.R
polish.pl		polish.pl
polish_assembly_with_ont_illumina.sh		polish_assembly_with_ont_illumina.sh
print_read_ids_multifast5.py		print_read_ids_multifast5.py
randomLines.pl		randomLines.pl
randomLinesHeader.pl		randomLinesHeader.pl
rapid_join_mod.pl		rapid_join_mod.pl
remove_Ns_from_illumina_pe_reads.pl		remove_Ns_from_illumina_pe_reads.pl
rename.pl		rename.pl
revcomp.pl		revcomp.pl
revcomp_agp.pl		revcomp_agp.pl
revcomp_scaffolds_from_list.pl		revcomp_scaffolds_from_list.pl
rsync_scratch_to_isilon.sh		rsync_scratch_to_isilon.sh
rsync_scratch_to_isilon_annotationdir.sh		rsync_scratch_to_isilon_annotationdir.sh
rsync_scratch_to_isilon_talioto.sh		rsync_scratch_to_isilon_talioto.sh
run_hifiasm_ont.sh		run_hifiasm_ont.sh

Repository files navigation

scripts

About

CNAG AAT scripts not guaranteed to work elsewhere

Custom properties

0 stars

4 watching

Report repository

Releases

Packages

Contributors

Languages