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directory_tree.txt
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.
|-- canu_job
| |-- 10_mummer
| | |-- consensus_pilon_HGAP_assembly.delta
| | |-- consensus_pilon_HGAP_assembly.filter
| | |-- consensus_pilon_HGAP_assembly.fplot
| | |-- consensus_pilon_HGAP_assembly.gp
| | |-- consensus_pilon_HGAP_assembly.png
| | |-- consensus_pilon_HGAP_assembly.rplot
| | |-- consensus_pilon_illumina_MPG_2013.delta
| | |-- consensus_pilon_illumina_MPG_2013.filter
| | |-- consensus_pilon_illumina_MPG_2013.fplot
| | |-- consensus_pilon_illumina_MPG_2013.gp
| | |-- consensus_pilon_illumina_MPG_2013.png
| | |-- consensus_pilon_illumina_MPG_2013.rplot
| | `-- mummer_plot.sh
| |-- 11_cdp
| | |-- cdf_graph.py
| | |-- CDF.png
| | `-- cdf.sh
| |-- 12_augustus
| | |-- augustus_consensus_pilon.fasta
| | |-- augustus_consensus_pilon.gff3
| | |-- augustus.sh
| | |-- augustus_stat_report.txt
| | |-- bedtools.sh
| | |-- consensus_pilon.fasta -> ../7_pilon/consensus_pilon.fasta
| | |-- consensus_pilon.fasta.fai
| | `-- trinityNx.sh
| |-- 2_unzip_pacbio
| | |-- 0001
| | | |-- Analysis_Results
| | | | |-- m130605_000141_42207_c100515142550000001823076608221372_s1_p0.1.bax.h5
| | | | |-- m130605_000141_42207_c100515142550000001823076608221372_s1_p0.2.bax.h5
| | | | |-- m130605_000141_42207_c100515142550000001823076608221372_s1_p0.3.bax.h5
| | | | |-- m130605_000141_42207_c100515142550000001823076608221372_s1_p0.bas.h5
| | | | `-- m130605_000141_42207_c100515142550000001823076608221372_s1_p0.fastq
| | | `-- m130605_000141_42207_c100515142550000001823076608221372_s1_p0.metadata.xml
| | |-- 0002
| | | |-- Analysis_Results
| | | | |-- m130605_032054_42207_c100515142550000001823076608221373_s1_p0.1.bax.h5
| | | | |-- m130605_032054_42207_c100515142550000001823076608221373_s1_p0.2.bax.h5
| | | | |-- m130605_032054_42207_c100515142550000001823076608221373_s1_p0.3.bax.h5
| | | | |-- m130605_032054_42207_c100515142550000001823076608221373_s1_p0.bas.h5
| | | | `-- m130605_032054_42207_c100515142550000001823076608221373_s1_p0.fastq
| | | `-- m130605_032054_42207_c100515142550000001823076608221373_s1_p0.metadata.xml
| | |-- 0007
| | | |-- Analysis_Results
| | | | |-- m130605_231954_42210_c100515112550000001823076608221304_s1_p0.1.bax.h5
| | | | |-- m130605_231954_42210_c100515112550000001823076608221304_s1_p0.2.bax.h5
| | | | |-- m130605_231954_42210_c100515112550000001823076608221304_s1_p0.3.bax.h5
| | | | |-- m130605_231954_42210_c100515112550000001823076608221304_s1_p0.bas.h5
| | | | `-- m130605_231954_42210_c100515112550000001823076608221304_s1_p0.fastq
| | | `-- m130605_231954_42210_c100515112550000001823076608221304_s1_p0.metadata.xml
| | |-- 0011
| | | |-- Analysis_Results
| | | | |-- m130607_031915_42207_c100539492550000001823089611241310_s1_p0.1.bax.h5
| | | | |-- m130607_031915_42207_c100539492550000001823089611241310_s1_p0.2.bax.h5
| | | | |-- m130607_031915_42207_c100539492550000001823089611241310_s1_p0.3.bax.h5
| | | | |-- m130607_031915_42207_c100539492550000001823089611241310_s1_p0.bas.h5
| | | | `-- m130607_031915_42207_c100539492550000001823089611241310_s1_p0.fastq
| | | `-- m130607_031915_42207_c100539492550000001823089611241310_s1_p0.metadata.xml
| | |-- 0012
| | | |-- Analysis_Results
| | | | |-- m130607_063829_42207_c100539492550000001823089611241311_s1_p0.1.bax.h5
| | | | |-- m130607_063829_42207_c100539492550000001823089611241311_s1_p0.2.bax.h5
| | | | |-- m130607_063829_42207_c100539492550000001823089611241311_s1_p0.3.bax.h5
| | | | |-- m130607_063829_42207_c100539492550000001823089611241311_s1_p0.bas.h5
| | | | `-- m130607_063829_42207_c100539492550000001823089611241311_s1_p0.fastq
| | | `-- m130607_063829_42207_c100539492550000001823089611241311_s1_p0.metadata.xml
| | |-- 0013
| | | |-- Analysis_Results
| | | | |-- m130607_131654_42207_c100539492550000001823089611241313_s1_p0.1.bax.h5
| | | | |-- m130607_131654_42207_c100539492550000001823089611241313_s1_p0.2.bax.h5
| | | | |-- m130607_131654_42207_c100539492550000001823089611241313_s1_p0.3.bax.h5
| | | | |-- m130607_131654_42207_c100539492550000001823089611241313_s1_p0.bas.h5
| | | | `-- m130607_131654_42207_c100539492550000001823089611241313_s1_p0.fastq
| | | `-- m130607_131654_42207_c100539492550000001823089611241313_s1_p0.metadata.xml
| | |-- 0014
| | | |-- Analysis_Results
| | | | |-- m130607_095747_42207_c100539492550000001823089611241312_s1_p0.1.bax.h5
| | | | |-- m130607_095747_42207_c100539492550000001823089611241312_s1_p0.2.bax.h5
| | | | |-- m130607_095747_42207_c100539492550000001823089611241312_s1_p0.3.bax.h5
| | | | |-- m130607_095747_42207_c100539492550000001823089611241312_s1_p0.bas.h5
| | | | `-- m130607_095747_42207_c100539492550000001823089611241312_s1_p0.fastq
| | | `-- m130607_095747_42207_c100539492550000001823089611241312_s1_p0.metadata.xml
| | |-- 0018
| | | |-- Analysis_Results
| | | | |-- m130609_051143_42207_c100539282550000001823089611241380_s1_p0.1.bax.h5
| | | | |-- m130609_051143_42207_c100539282550000001823089611241380_s1_p0.2.bax.h5
| | | | |-- m130609_051143_42207_c100539282550000001823089611241380_s1_p0.3.bax.h5
| | | | |-- m130609_051143_42207_c100539282550000001823089611241380_s1_p0.bas.h5
| | | | `-- m130609_051143_42207_c100539282550000001823089611241380_s1_p0.fastq
| | | `-- m130609_051143_42207_c100539282550000001823089611241380_s1_p0.metadata.xml
| | |-- 0019
| | | |-- Analysis_Results
| | | | |-- m130609_050958_42210_c100539382550000001823089611241350_s1_p0.1.bax.h5
| | | | |-- m130609_050958_42210_c100539382550000001823089611241350_s1_p0.2.bax.h5
| | | | |-- m130609_050958_42210_c100539382550000001823089611241350_s1_p0.3.bax.h5
| | | | |-- m130609_050958_42210_c100539382550000001823089611241350_s1_p0.bas.h5
| | | | `-- m130609_050958_42210_c100539382550000001823089611241350_s1_p0.fastq
| | | `-- m130609_050958_42210_c100539382550000001823089611241350_s1_p0.metadata.xml
| | |-- 0020
| | | |-- Analysis_Results
| | | | |-- m130609_083056_42207_c100539282550000001823089611241381_s1_p0.1.bax.h5
| | | | |-- m130609_083056_42207_c100539282550000001823089611241381_s1_p0.2.bax.h5
| | | | |-- m130609_083056_42207_c100539282550000001823089611241381_s1_p0.3.bax.h5
| | | | |-- m130609_083056_42207_c100539282550000001823089611241381_s1_p0.bas.h5
| | | | `-- m130609_083056_42207_c100539282550000001823089611241381_s1_p0.fastq
| | | `-- m130609_083056_42207_c100539282550000001823089611241381_s1_p0.metadata.xml
| | `-- 0021
| | |-- Analysis_Results
| | | |-- m130609_082855_42210_c100539382550000001823089611241351_s1_p0.1.bax.h5
| | | |-- m130609_082855_42210_c100539382550000001823089611241351_s1_p0.2.bax.h5
| | | |-- m130609_082855_42210_c100539382550000001823089611241351_s1_p0.3.bax.h5
| | | |-- m130609_082855_42210_c100539382550000001823089611241351_s1_p0.bas.h5
| | | `-- m130609_082855_42210_c100539382550000001823089611241351_s1_p0.fastq
| | `-- m130609_082855_42210_c100539382550000001823089611241351_s1_p0.metadata.xml
| |-- 4_merged_fastq
| | `-- yeast.fastq
| |-- 5_canu
| | |-- 5_canu.contigs.fasta
| | |-- 5_canu.contigs.gfa
| | |-- 5_canu.contigs.layout
| | |-- 5_canu.contigs.layout.readToTig
| | |-- 5_canu.contigs.layout.tigInfo
| | |-- 5_canu.correctedReads.fasta.gz
| | |-- 5_canu.report
| | |-- 5_canu.seqStore.err
| | |-- 5_canu.seqStore.ssi
| | |-- 5_canu.trimmedReads.fasta.gz
| | |-- 5_canu.unassembled.fasta
| | |-- 5_canu.unitigs.bed
| | |-- 5_canu.unitigs.fasta
| | |-- 5_canu.unitigs.gfa
| | |-- 5_canu.unitigs.layout
| | |-- 5_canu.unitigs.layout.readToTig
| | |-- 5_canu.unitigs.layout.tigInfo
| | |-- canu-logs
| | |-- canu-scripts
| | |-- haplotype
| | `-- tree
| |-- 6_quiver
| | |-- 2_unzip_pacbio -> ../2_unzip_pacbio
| | |-- 5_canu.contigs.fasta -> ../5_canu/5_canu.contigs.fasta
| | |-- 5_canu.contigs.fasta.fai
| | |-- consensus.fasta
| | |-- consensus.fastq
| | |-- input_0001.fofn
| | |-- input_0002.fofn
| | |-- input_0007.fofn
| | |-- input_0011.fofn
| | |-- input_0012.fofn
| | |-- input_0013.fofn
| | |-- input_0014.fofn
| | |-- input_0018.fofn
| | |-- input_0019.fofn
| | |-- input_0020.fofn
| | |-- input_0021.fofn
| | |-- input_master.fofn
| | |-- merge_cmp_h5.sh
| | |-- myjoblist.txt
| | |-- out_0001.cmp.h5
| | |-- out_0002.cmp.h5
| | |-- out_0007.cmp.h5
| | |-- out_0011.cmp.h5
| | |-- out_0012.cmp.h5
| | |-- out_0013.cmp.h5
| | |-- out_0014.cmp.h5
| | |-- out_0018.cmp.h5
| | |-- out_0019.cmp.h5
| | |-- out_0020.cmp.h5
| | |-- out_0021.cmp.h5
| | |-- out_all.cmp.h5
| | |-- pbalign.sh
| | |-- prep_cmp_h5.sh
| | |-- quiver_run.sh
| | `-- variants.gff
| |-- 7_pilon
| | |-- bowtie2.sh
| | |-- bowtie_build.sh
| | |-- consensus.1.bt2
| | |-- consensus.2.bt2
| | |-- consensus.3.bt2
| | |-- consensus.4.bt2
| | |-- consensus.fasta -> ../6_quiver/consensus.fasta
| | |-- consensus.fasta.fai
| | |-- consensus_pilonBadCoverage.wig
| | |-- consensus_pilonChanges.wig
| | |-- consensus_pilonClippedAlignments.wig
| | |-- consensus_pilonCopyNumber.wig
| | |-- consensus_pilonCoverage.wig
| | |-- consensus_pilonDeltaCoverage.wig
| | |-- consensus_pilonDipCoverage.wig
| | |-- consensus_pilon.fasta
| | |-- consensus_pilonGC.wig
| | |-- consensus_pilonPctBad.wig
| | |-- consensus_pilonPhysicalCoverage.wig
| | |-- consensus_pilonPilon.bed
| | |-- consensus_pilonUnconfirmed.wig
| | |-- consensus_pilon.vcf
| | |-- consensus_pilonWeightedMq.wig
| | |-- consensus_pilonWeightedQual.wig
| | |-- consensus.rev.1.bt2
| | |-- consensus.rev.2.bt2
| | |-- pilon_run.sh
| | |-- samtools.sh
| | |-- SRR1569900_1.fastq -> ../../rawdata/illumina/SRR1569900_1.fastq
| | |-- SRR1569900_2.fastq -> ../../rawdata/illumina/SRR1569900_2.fastq
| | |-- W303_consensus.bam
| | |-- W303_consensus.sam
| | |-- W303_consensus_sorted.bai
| | `-- W303_consensus_sorted.bam
| |-- 8_quast
| | |-- quast_result
| | | |-- basic_stats
| | | | |-- consensus_pilon_GC_content_plot.pdf
| | | | |-- cumulative_plot.pdf
| | | | |-- GC_content_plot.pdf
| | | | |-- HGAP_assembly_GC_content_plot.pdf
| | | | |-- illumina_MPG_2013_contig_GC_content_plot.pdf
| | | | `-- Nx_plot.pdf
| | | |-- icarus.html
| | | |-- icarus_viewers
| | | | `-- contig_size_viewer.html
| | | |-- quast.log
| | | |-- report.html
| | | |-- report.pdf
| | | |-- report.tex
| | | |-- report.tsv
| | | |-- report.txt
| | | |-- transposed_report.tex
| | | |-- transposed_report.tsv
| | | `-- transposed_report.txt
| | `-- quast.sh
| `-- 9_busco
| |-- busco.sh
| |-- run_9_busco_Final_Assembly
| | |-- angustus_output
| | |-- blask_output
| | |-- full_table_9_busco_Final_Assembly.tsv
| | |-- hmmer_output
| | |-- missing_busco_list_9_busco_Final_Assembly.tsv
| | |-- short_summary_9_busco_Final_Assembly.txt
| | `-- single_copy_busco_sequences
| `-- tmp
|-- canu_run.sh
|-- create_folder.sh
|-- directory_tree.txt
|-- download_data.sh
|-- generate_fastq.sh
`-- rawdata
|-- busco
| |-- saccharomycetales_odb9
| | |-- ancestral
| | |-- ancestral_variants
| | |-- dataset.cfg
| | |-- hmms
| | |-- info
| | |-- lengths_cutoff
| | |-- prfl
| | `-- scores_cutoff
| `-- saccharomycetales_odb9.tar.gz
|-- illumina
| |-- SRR1569900_1.fastq
| `-- SRR1569900_2.fastq
`-- REF
|-- HGAP_assembly.fasta
|-- illumina_MPG_2013_contig.fasta
|-- illumina_MPG_2013.fasta
|-- separate_short_read_contigs.py
`-- separate_short_read_contigs.sh
54 directories, 217 files