From f2cdb0d1966f2a4d4550543b3cd7678d123dbed2 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 3 Dec 2024 12:50:38 -0500 Subject: [PATCH] Update README.md --- .../Scaffolding-HiC-VGP8/README.md | 28 ++++++++++--------- 1 file changed, 15 insertions(+), 13 deletions(-) diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/README.md b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/README.md index e497e5704..79b1ee816 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/README.md +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/README.md @@ -9,21 +9,23 @@ Example of trajectory : ## Inputs -1. Scaffolded assembly [fasta] -2. Database for busco lineage (recommended: latest) -3. Busco lineage (recommended: vertebrata) -4. Concatenated HiC forward reads [fastq] -5. Concatenated HiC reverse reads [fastq] -6. Restriction enzyme sequence (recommended for VGP data: Arima Hi-C 2.0) -7. Estimated genome size [txt] -8. Haplotype name +1. Scaffolded assembly [gfa] +2. Name of the haplotype +3. HiC forward reads [fastq] +4. HiC reverse reads [fastq] +5. Trim Hi-C data? If `yes` Trim 5 bases at the beginning of each read. Use with Arima Hi-C data if the Hi-C map looks "noisy". +6. Database for busco lineage (recommended: latest) +7. Busco lineage (recommended: vertebrata) +8. Restriction enzyme sequence (recommended for VGP data: Arima Hi-C 2.0) +9. Estimated genome size [txt] ### Outputs 1. Scaffolds in [fasta] and [gfa] format -2. QC: Assembly statistics -3. QC: Nx plot -4. QC: Size plot -5. QC: BUSCO report -6. QC: Pretext Maps before and after scaffolding \ No newline at end of file +2. If you selected `yes` for Hi-C trimming, the trimmed collections of Hi-C reads +3. QC: Assembly statistics +4. QC: Nx plot +5. QC: Size plot +6. QC: BUSCO report +7. QC: Pretext Maps before and after scaffolding