Initial commit

.editorconfig

+# EditorConfig is awesome: https://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+# Unix-style newlines with a newline ending every file
+[*]
+charset = utf-8
+end_of_line = lf
+indent_size = 4
+indent_style = space
+insert_final_newline = true
+
+[*.{c,h,cpp,hpp,d,sh,py,pl}]
+max_line_length = 100
+
+[Makefile]
+indent_style = tab
+
+[*.yml]
+indent_size = 2

.gitignore

+/assembly
+/data
+/processed-data
+/mapping
+*.dat
+*.exe
+*.fasta
+*.fasta.gz
+*.log
+*.o
+*.obj
+*.pdf
+*.sublime-*
+*.tar
+*.tar.gz
+*~
+__pycache__

LICENSE

+MIT License
+
+Copyright (c) 2020 assembly
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

QC/bionano/.keep

+

README.md

+# asm_wPlaDum *de novo* genome assembly
+
+HiFi + HiC assembly (Jochen Rink)
+
+## General Info
+
+* Project: NGS-CC
+* Species: Platynereis dumerilii (Dumeril's clam worm)
+* Estimated genome size: 900M
+* Classification: [NCBI taxonomy](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=6359)
+* NCBI taxonomy ID: 6359
+
+![Platynereis dumerilii](images/platynereis_dumerilii.jpg)
+
+# PacBio_lofisummary
+
+# PacBio_hifisummary
+
+# BioNano_summary
+
+# 10X_summary
+
+## Genomescope
+
+## LongRanger
+
+-------------------------------------------------------------------------------------------------------

README.template.md

+# {{PROJECT_ID}} *de novo* genome assembly
+
+{{PROJECT_DESCRIPTION}}
+
+## General Info
+
+* Project: {{PROJECT_SOURCE}}
+* Species: {{SPECIES_FULL_SCIENTIFIC_NAME}} ({{SPECIES_FULL_TRIVIAL_NAME}})
+* Estimated genome size: {{GENOME_SIZE}}
+* Classification: [NCBI taxonomy](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id={{NCBI_TAXONOMY_ID}})
+* NCBI taxonomy ID: {{NCBI_TAXONOMY_ID}}
+
+![{{SPECIES_FULL_SCIENTIFIC_NAME}}](images/{{SPECIES_ID}}.jpg)
+
+# PacBio_lofisummary
+
+# PacBio_hifisummary
+
+# BioNano_summary
+
+# 10X_summary
+
+## Genomescope
+
+## LongRanger
+
+-------------------------------------------------------------------------------------------------------