results_archive_incl.txt 4.24 KB
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# preprocessing stats
preproc/metag/sr/fastp.html
preproc/metag/sr/fastp.tsv
preproc/metat/sr/fastp.html
preproc/metat/sr/fastp.tsv
preproc/metag/lr/bbmap.host.stats
preproc/metag/sr/bbmap.host.stats
preproc/metat/sr/bbmap.host.stats
preproc/metat/sr/bbmap.rrna.stats
# reads QC
qc/metag/sr/R1.fastp_fastqc.zip
qc/metag/sr/R2.fastp_fastqc.zip
qc/metat/sr/R1.fastp_fastqc.zip
qc/metat/sr/R2.fastp_fastqc.zip
qc/metag/lr/NanoStats.tsv
qc/metag/lr/NanoStats.txt
# assembly: raw, polished, polishing steps
assembly/hy/metaspadeshybrid/ASSEMBLY.fasta
assembly/hy/metaspadeshybrid/ASSEMBLY.POLISHED.fasta
assembly/hy/operamsmegahit/ASSEMBLY.fasta
assembly/hy/operamsmegahit/ASSEMBLY.POLISHED.fasta
assembly/hy/operamsmetaspades/ASSEMBLY.fasta
assembly/hy/operamsmetaspades/ASSEMBLY.POLISHED.fasta
assembly/lr/flye/ASSEMBLY.fasta
assembly/lr/flye/ASSEMBLY.POLISHED.fasta
assembly/lr/raven/ASSEMBLY.fasta
assembly/lr/raven/ASSEMBLY.POLISHED.fasta
assembly/sr/megahit/ASSEMBLY.fasta
assembly/sr/metaspades/ASSEMBLY.fasta
# mapping: metag
mapping/metag/mappability.tsv
# mapping: metat
mapping/metat/mappability.tsv
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mapping/metat/hy/metaspadeshybrid/ASSEMBLY.POLISHED.sr.cov.pergene
mapping/metat/hy/operamsmegahit/ASSEMBLY.POLISHED.sr.cov.pergene
mapping/metat/hy/operamsmetaspades/ASSEMBLY.POLISHED.sr.cov.pergene
mapping/metat/lr/flye/ASSEMBLY.POLISHED.sr.cov.pergene
mapping/metat/lr/raven/ASSEMBLY.POLISHED.sr.cov.pergene
mapping/metat/sr/megahit/ASSEMBLY.POLISHED.sr.cov.pergene
mapping/metat/sr/metaspades/ASSEMBLY.POLISHED.sr.cov.pergene
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# annotation: prodigal
annotation/prodigal/hy/metaspadeshybrid/proteins.faa
annotation/prodigal/hy/operamsmegahit/proteins.faa
annotation/prodigal/hy/operamsmetaspades/proteins.faa
annotation/prodigal/lr/flye/proteins.faa
annotation/prodigal/lr/raven/proteins.faa
annotation/prodigal/sr/megahit/proteins.faa
annotation/prodigal/sr/metaspades/proteins.faa
annotation/prodigal/summary.gene.counts.tsv
annotation/prodigal/summary.gene.length.tsv
# annotation: rgi
annotation/rgi/hy/metaspadeshybrid/rgi.txt
annotation/rgi/hy/operamsmegahit/rgi.txt
annotation/rgi/hy/operamsmetaspades/rgi.txt
annotation/rgi/lr/flye/rgi.txt
annotation/rgi/lr/raven/rgi.txt
annotation/rgi/sr/megahit/rgi.txt
annotation/rgi/sr/metaspades/rgi.txt
annotation/rgi/summary.tsv
# annotation: barrnap
annotation/barrnap/hy/metaspadeshybrid/*.gff
annotation/barrnap/hy/operamsmegahit/*.gff
annotation/barrnap/hy/operamsmetaspades/*.gff
annotation/barrnap/lr/flye/*.gff
annotation/barrnap/lr/raven/*.gff
annotation/barrnap/sr/megahit/*.gff
annotation/barrnap/sr/metaspades/*.gff
annotation/barrnap/summary.tsv
# analysis
analysis/quast/hy/metaspadeshybrid/report.tsv
analysis/quast/hy/operamsmegahit/report.tsv
analysis/quast/hy/operamsmetaspades/report.tsv
analysis/quast/lr/flye/report.tsv
analysis/quast/lr/raven/report.tsv
analysis/quast/sr/megahit/report.tsv
analysis/quast/sr/metaspades/report.tsv
analysis/quast/summary_report.tsv
analysis/mash/contigs.*
analysis/diamond/hy_metaspadeshybrid.tsv
analysis/diamond/hy_operamsmegahit.tsv
analysis/diamond/hy_operamsmetaspades.tsv
analysis/diamond/lr_flye.tsv
analysis/diamond/lr_raven.tsv
analysis/diamond/sr_megahit.tsv
analysis/diamond/sr_metaspades.tsv
analysis/diamond/summary.db.tsv
analysis/mmseqs2/clusters.tsv
analysis/mmseqs2/summary.tsv
# GDB metaP reports
metap/20210323/flye_1_1_Default_Peptide_Report.txt
metap/20210323/flye_1_1_Default_Protein_Report.txt
metap/20210323/megahit_1_1_Default_Peptide_Report.txt
metap/20210323/megahit_1_1_Default_Protein_Report.txt
metap/20210323/metaspades_1_1_Default_Peptide_Report.txt
metap/20210323/metaspades_1_1_Default_Protein_Report.txt
metap/20210323/metaspadeshybrid_1_1_Default_Peptide_Report.txt
metap/20210323/metaspadeshybrid_1_1_Default_Protein_Report.txt
metap/20210323/operamsmegahit_1_1_Default_Peptide_Report.txt
metap/20210323/operamsmegahit_1_1_Default_Protein_Report.txt
metap/20210323/operamsmetaspades_1_1_Default_Peptide_Report.txt
metap/20210323/operamsmetaspades_1_1_Default_Protein_Report.txt
metap/20210323/proteins_1_1_Default_Peptide_Report.txt
metap/20210323/proteins_1_1_Default_Protein_Report.txt
metap/20210323/raven_1_1_Default_Peptide_Report.txt
metap/20210323/raven_1_1_Default_Protein_Report.txt
# GDB extra analysis
report/amr.tsv
report/mmseqs2_highconf.tsv
report/mmseqs2_uniq.tsv
report/metap.txt