Commit 24309570 authored by Valentina Galata's avatar Valentina Galata
Browse files

readme/archive: rm large files from results archive

parent 3fc1b86c
......@@ -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
......
......@@ -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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