https://github.com/brocklab/clonmapper-sequencing
Science Score: 13.0%
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○CITATION.cff file
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○.zenodo.json file
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○Scientific vocabulary similarity
Low similarity (8.1%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: brocklab
- Language: Python
- Default Branch: main
- Size: 13.7 KB
Statistics
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
ClonMapper Sequencing
Repo to generate the necessary oligo sequences for target sequencing of ClonMapper-labeled cells.
Requirements
python> 3.7
Setup
Start by cloning the repo.
bash
git clone git@github.com:brocklab/clonmapper-sequencing.git
Generating sequences
To generate a list of sequences edit the indices.csv file and execute the script.
Only the "type" and "sequence" columns are considered. Any additional columns are ignored.
bash
./generate-oligos
The i7 sequences should be as they will appear on the sample sheet not within the sequence. The script will automatically generate the reverse complement prior to adding it.
There are a number of supported output formats.
All of which are plain text. You can specify a tsv or csv which may be useful in ordering. Additionally you can output a genbank file for each sequence individually or all sequences in a single genbank file.
Sequences
Sequences should be input as they would appear in your submitted sample sheet.
As described by NEB:
Reverse Strand Workflow for the following instruments: iSeq 100, MiniSeq with standard reagent kits, NextSeq Systems, NovaSeq 6000 with v1.5 reagent kits, HiSeq 2000/5000 (single-read flow cell), HiSeq 3000/4000 (paired-end flow cell)
Resources
See Illumina for list of typical indices.
Owner
- Name: brocklab
- Login: brocklab
- Kind: organization
- Location: Austin, TX
- Website: http://www.brocklab.com/
- Repositories: 4
- Profile: https://github.com/brocklab