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ONT_pilot_gitlab
Commits
24309570
Commit
24309570
authored
Apr 19, 2021
by
Valentina Galata
Browse files
readme/archive: rm large files from results archive
parent
3fc1b86c
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2
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README_ARCHIVE.md
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24309570
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@@ -25,9 +25,7 @@ For each sample, the following files were saved (in `<sample>/results/`):
-
assembly
-
"raw" contigs:
`assembly/*/*/ASSEMBLY.fasta`
-
polished contigs:
`assembly/*/*/ASSEMBLY.POLISHED.fasta`
(for LR and Hy only)
-
polishing rounds:
`assembly/*/*/POLISHING_*/ASSEMBLY.fasta`
-
assembly mapping
-
BAM files:
`mapping/*/*/*/ASSEMBLY.POLISHED.*.bam`
-
mapping rate summary stats:
`mapping/*/mappability.tsv`
-
annotation
-
protein prediction w/ Prodigal
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config/archive/results_archive_incl.txt
View file @
24309570
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@@ -17,60 +17,19 @@ qc/metag/lr/NanoStats.txt
# assembly: raw, polished, polishing steps
assembly/hy/metaspadeshybrid/ASSEMBLY.fasta
assembly/hy/metaspadeshybrid/ASSEMBLY.POLISHED.fasta
assembly/hy/metaspadeshybrid/POLISHING_raconSR1/ASSEMBLY.fasta
assembly/hy/metaspadeshybrid/POLISHING_raconSR2/ASSEMBLY.fasta
assembly/hy/metaspadeshybrid/POLISHING_raconSR3/ASSEMBLY.fasta
assembly/hy/metaspadeshybrid/POLISHING_raconSR4/ASSEMBLY.fasta
assembly/hy/metaspadeshybrid/POLISHING_raconSR5/ASSEMBLY.fasta
assembly/hy/operamsmegahit/ASSEMBLY.fasta
assembly/hy/operamsmegahit/ASSEMBLY.POLISHED.fasta
assembly/hy/operamsmegahit/POLISHING_raconSR1/ASSEMBLY.fasta
assembly/hy/operamsmegahit/POLISHING_raconSR2/ASSEMBLY.fasta
assembly/hy/operamsmegahit/POLISHING_raconSR3/ASSEMBLY.fasta
assembly/hy/operamsmegahit/POLISHING_raconSR4/ASSEMBLY.fasta
assembly/hy/operamsmegahit/POLISHING_raconSR5/ASSEMBLY.fasta
assembly/hy/operamsmetaspades/ASSEMBLY.fasta
assembly/hy/operamsmetaspades/ASSEMBLY.POLISHED.fasta
assembly/hy/operamsmetaspades/POLISHING_raconSR1/ASSEMBLY.fasta
assembly/hy/operamsmetaspades/POLISHING_raconSR2/ASSEMBLY.fasta
assembly/hy/operamsmetaspades/POLISHING_raconSR3/ASSEMBLY.fasta
assembly/hy/operamsmetaspades/POLISHING_raconSR4/ASSEMBLY.fasta
assembly/hy/operamsmetaspades/POLISHING_raconSR5/ASSEMBLY.fasta
assembly/lr/flye/ASSEMBLY.fasta
assembly/lr/flye/ASSEMBLY.POLISHED.fasta
assembly/lr/flye/POLISHING_raconLR1/ASSEMBLY.fasta
assembly/lr/flye/POLISHING_raconLR1_raconSR1/ASSEMBLY.fasta
assembly/lr/flye/POLISHING_raconLR1_raconSR2/ASSEMBLY.fasta
assembly/lr/flye/POLISHING_raconLR1_raconSR3/ASSEMBLY.fasta
assembly/lr/flye/POLISHING_raconLR1_raconSR4/ASSEMBLY.fasta
assembly/lr/flye/POLISHING_raconLR1_raconSR4_medakaLR1/ASSEMBLY.fasta
assembly/lr/raven/ASSEMBLY.fasta
assembly/lr/raven/ASSEMBLY.POLISHED.fasta
assembly/lr/raven/POLISHING_raconLR1/ASSEMBLY.fasta
assembly/lr/raven/POLISHING_raconLR1_raconSR1/ASSEMBLY.fasta
assembly/lr/raven/POLISHING_raconLR1_raconSR2/ASSEMBLY.fasta
assembly/lr/raven/POLISHING_raconLR1_raconSR3/ASSEMBLY.fasta
assembly/lr/raven/POLISHING_raconLR1_raconSR4/ASSEMBLY.fasta
assembly/lr/raven/POLISHING_raconLR1_raconSR4_medakaLR1/ASSEMBLY.fasta
assembly/sr/megahit/ASSEMBLY.fasta
assembly/sr/metaspades/ASSEMBLY.fasta
# mapping: metag
mapping/metag/hy/metaspadeshybrid/ASSEMBLY.POLISHED.hy.bam
mapping/metag/hy/operamsmegahit/ASSEMBLY.POLISHED.hy.bam
mapping/metag/hy/operamsmetaspades/ASSEMBLY.POLISHED.hy.bam
mapping/metag/lr/flye/ASSEMBLY.POLISHED.lr.bam
mapping/metag/lr/raven/ASSEMBLY.POLISHED.lr.bam
mapping/metag/sr/megahit/ASSEMBLY.POLISHED.sr.bam
mapping/metag/sr/metaspades/ASSEMBLY.POLISHED.sr.bam
mapping/metag/mappability.tsv
# mapping: metat
mapping/metat/hy/metaspadeshybrid/ASSEMBLY.POLISHED.sr.bam
mapping/metat/hy/operamsmegahit/ASSEMBLY.POLISHED.sr.bam
mapping/metat/hy/operamsmetaspades/ASSEMBLY.POLISHED.sr.bam
mapping/metat/lr/flye/ASSEMBLY.POLISHED.sr.bam
mapping/metat/lr/raven/ASSEMBLY.POLISHED.sr.bam
mapping/metat/sr/megahit/ASSEMBLY.POLISHED.sr.bam
mapping/metat/sr/metaspades/ASSEMBLY.POLISHED.sr.bam
mapping/metat/mappability.tsv
# annotation: prodigal
annotation/prodigal/hy/metaspadeshybrid/proteins.faa
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