https://github.com/barricklab/madcap-seq
Scripts to analyze multiplex adaptome sequencing data
https://github.com/barricklab/madcap-seq
bioinformatics evolution genomics
Last synced: 4 months ago
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Scripts to analyze multiplex adaptome sequencing data
- Host: GitHub
- URL: https://github.com/barricklab/madcap-seq
- Owner: barricklab
- License: mit
- Created: 2020-06-20T12:19:32.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2021-07-12T15:21:14.000Z (about 5 years ago)
- Last Synced: 2025-09-09T13:54:11.387Z (11 months ago)
- Topics: bioinformatics, evolution, genomics
- Language: R
- Homepage:
- Size: 3.13 MB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Multiplex Adaptome Capture Sequencing (mAdCap-Seq)
Scripts and data files for the analysis pipeline described in **"High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture sequencing"**.
## Overview
* `reference` contains sequence files for the targeted genes of interest and the _E. coli_ REL606 genome with these regions masked out.
* `consensus_read_generation` has the script for using unique molecular identifiers to perform error correction on raw Illumina reads.
* `breseq_postprocessing` has the script for converting raw output generated by running [_breseq_](https://github.com/barricklab/breseq) on these files into a format with the read counts supporting the reference versus variant alleles.
* `trajectory_analysis` contains the main scripts for filtering and analyzing the trajectories of mutation frequencies.
* `LTEE-compare` and `protein_structure` contain scripts and information for further analyzing the sets of predicted mutations.