Copycat
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 upload to SplitThreader) and in a .seg format (for viewing the copy number profile in IGV)
| Project Name | Stars | Downloads | Repos Using This | Packages Using This | Most Recent Commit | Total Releases | Latest Release | Open Issues | License | Language |
|---|---|---|---|---|---|---|---|---|---|---|
| Mosdepth | 617 | 6 months ago | 49 | mit | Nim | |||||
| fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing | ||||||||||
| Coverm | 237 |  | 1 | 4 months ago | 9 | February 24, 2021 | 50 | gpl-3.0 | Rust | |
| Read coverage calculator for metagenomics | ||||||||||
| Smudgeplot | 200 | 4 months ago | 19 | apache-2.0 | R | |||||
| Inference of ploidy and heterozygosity structure using whole genome sequencing data | ||||||||||
| Rasusa | 156 | 5 months ago | 11 | April 06, 2023 | 3 | mit | Rust | |||
| Randomly subsample sequencing reads to a specified coverage | ||||||||||
| Estimate_genome_size.pl | 53 | a year ago | 6 | Perl | ||||||
| Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish | ||||||||||
| Cnview | 50 | 6 years ago | 3 | mit | R | |||||
| Visualization and annotation of CNVs from population-scale whole-genome sequencing data | ||||||||||
| Physalia Lcwgs | 43 | 8 months ago | HTML | |||||||
| Files for the the Physalia course on Population genomic inference from low-coverage whole-genome sequencing data, Oct 10-13, 2022 | ||||||||||
| Seqcover | 38 | 3 years ago | 3 | mit | Nim | |||||
| seqcover allows user to view coverage for hundreds of genes and dozens of samples | ||||||||||
| Ploidyngs | 35 | a year ago | 1 | gpl-3.0 | HTML | |||||
| Explore ploidy levels from NGS data alone | ||||||||||
| Organelle_pba | 23 | 6 years ago | 8 | Perl | ||||||
| A software to assemble chloroplast and mitochodrial genomes using PacBio data | ||||||||||
Alternatives To CopycatSelect To Compare
Alternative Project Comparisons
Popular Genome Projects
Popular Code Coverage Projects
Popular Science Categories
Get A Weekly Email With Trending Projects For These Categories
No Spam. Unsubscribe easily at any time.
Shell
Code Coverage
Genome