Copycat is a simple script to capture and bin the read coverage across a genome from a bam file of read alignments. It relies on bedtools to get coverage for each individual nucleotide in the genome using bedtools genomecov, then bins and organizes these coverage values into 10kb bins and outputs the coverage information in a .csv format (for …
☆17Aug 24, 2016Updated 9 years ago
Alternatives and similar repositories for copycat
Users that are interested in copycat are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Creates an N-chart for comparing assembly lengths, including script for counting assembly lengths from a fasta file☆13Feb 2, 2017Updated 9 years ago
- SplitThreader has moved into Ribbon!☆67Aug 28, 2024Updated last year
- A tutorial in Python where all the examples teach students about biology. Written for high school students with no previous experience.☆19Aug 15, 2015Updated 10 years ago
- Run and Analyse SLiM Population Genetics Forward Simulations from R.☆10Nov 26, 2025Updated 3 months ago
- convert alignment bam to pairwise alignment or multiple sequence alignment (msa) at genome specific region☆13May 21, 2024Updated last year
- Scripts and data for Plotting in R for Biologists, a video course on YouTube☆61Sep 10, 2020Updated 5 years ago
- Analysis scripts from the paper "Eight thousand years of natural selection in Europe".☆11Nov 19, 2015Updated 10 years ago
- Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference gen…☆147Updated this week
- A genome browser designed for complex structural variants and long reads.☆298Jun 6, 2025Updated 9 months ago
- PhenoSV: Interpretable phenotype-aware model for the prioritization of genes affected by structural variants.☆17Feb 11, 2025Updated last year
- structure detection program☆18Nov 20, 2024Updated last year
- Annotation of cryptic transposon variants using Hidden Markov Models to detect conserved terminal features.☆10Jan 27, 2026Updated last month
- Linear-time, low-memory construction of variation graphs☆20Feb 3, 2020Updated 6 years ago
- A script to extract graph structure from multiple sequence alignment result and output as GFA/JSON for vg☆11Mar 27, 2019Updated 6 years ago
- ☆13Mar 7, 2021Updated 5 years ago
- A tool to calculate ploidy levels from genotype likelihoods and coverage using Hidden Markov Models☆18Nov 29, 2022Updated 3 years ago
- Population genetics analysis on VG☆17Apr 22, 2021Updated 4 years ago
- Distinguishing among modes of convergent adaptation using population genomic data: statistical inference method, extensions, and examples☆13May 1, 2019Updated 6 years ago
- Dot: An interactive dot plot viewer for comparative genomics☆36May 4, 2023Updated 2 years ago
- ☆15Jun 6, 2023Updated 2 years ago
- Bioinformatics scripts for genome analysis☆17Oct 26, 2022Updated 3 years ago
- Convert structural variants to sequence graphs [ VCF + FASTA ---> GFA ]☆11Mar 6, 2024Updated 2 years ago
- Code and Tutorials for Running the MArginal ePIstasis Test (MAPIT)☆19Nov 29, 2022Updated 3 years ago
- A wrapper for calling small variants from human germline high-coverage single-sample Illumina data☆14Jul 21, 2019Updated 6 years ago
- ☆78Jul 12, 2023Updated 2 years ago
- Kmer based genotyper for short reads.☆23Oct 19, 2021Updated 4 years ago
- Divine: Prioritizing Genes for Rare Mendelian Disease in Whole Exome Sequencing Data☆13Apr 18, 2019Updated 6 years ago
- ☆12Dec 26, 2018Updated 7 years ago
- ☆24May 22, 2025Updated 10 months ago
- A small R notebook describing how plot common (aDNA) population genetics PCAs using R and the tidyverse.☆14May 3, 2019Updated 6 years ago
- ☆10Aug 12, 2024Updated last year
- ☆13Aug 8, 2021Updated 4 years ago
- a tool for summarizing and integrating gene-set analysis results☆16Aug 14, 2024Updated last year
- heuristics to merge structural variant calls in VCF format.☆38Oct 6, 2016Updated 9 years ago
- Translocator: local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long read…☆12Jan 22, 2020Updated 6 years ago
- POSTRE: Prediction Of STRuctural variant Effects☆28Jan 9, 2026Updated 2 months ago
- Extra add-ons that may be useful for people using SLiM, but that are not part of the SLiM project itself☆44Oct 30, 2025Updated 4 months ago
- Genomic data interpretation and visualization Workshop☆22Updated this week
- ☆16Feb 11, 2022Updated 4 years ago