fbreitwieser / bamcovView external linksLinks
Quickly calculate and visualize sequence coverage in alignment files
☆100Jun 22, 2019Updated 6 years ago
Alternatives and similar repositories for bamcov
Users that are interested in bamcov are comparing it to the libraries listed below
Sorting:
- A read extraction and realignment tool for next generation sequencing data☆104Oct 29, 2022Updated 3 years ago
- Somatic (mosaic) SNV caller for 10X Genomics data using random forest classification and feature-based filters☆23Apr 1, 2019Updated 6 years ago
- Genome inference from a population reference graph☆96Apr 1, 2025Updated 10 months ago
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆143Aug 24, 2025Updated 5 months ago
- Accurate and fast taxonomic classification using pseudoaligning☆21Sep 16, 2017Updated 8 years ago
- Peregrine: Fast Genome Assembler Using SHIMMER Index☆102Feb 6, 2022Updated 4 years ago
- a toolset for efficient analysis of 10X Genomics linked read data sets, in particular for de novo assembly☆15Nov 27, 2019Updated 6 years ago
- Collection of simple C scripts for parsing vcf or bam files using the htslib C library. These scripts can be used as the starting point f…☆11Dec 11, 2020Updated 5 years ago
- Pan-genome inference and genotyping with long noisy or short accurate reads☆119Dec 13, 2024Updated last year
- SRF: Satellite Repeat Finder☆101Jan 8, 2024Updated 2 years ago
- Toolkit for VNTR genotyping and repeat-pan genome graph construction☆31Aug 18, 2025Updated 5 months ago
- PanEffect is a JavaScript framework to explore variant effects across a pangenome. The tool has two views that allows a user to (1) expl…☆13Jan 30, 2024Updated 2 years ago
- Efficient C functions to compute the summary statistics (flagstats) for sequencing read sets.☆15Dec 16, 2019Updated 6 years ago
- ☆26Aug 10, 2021Updated 4 years ago
- An Artificial Neural Network-based discriminator for validating clinically significant genomic variants☆35Dec 25, 2023Updated 2 years ago
- Ximmer is a system for CNV calling on exome and targeted genomic sequencing☆19Jan 28, 2026Updated 2 weeks ago
- Hidden Markov Model based Copy number caller☆20Dec 9, 2025Updated 2 months ago
- A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region exp…☆27Jan 15, 2026Updated last month
- ClaMSA (Classify Multiple Sequence Alignments).☆13Nov 21, 2024Updated last year
- Split a BAM file by haplotype support☆16Dec 13, 2017Updated 8 years ago
- BigWig and BAM utilities☆102Mar 26, 2024Updated last year
- De novo estimates of genetic relatedness from next-gen sequencing data☆45Jul 28, 2019Updated 6 years ago
- Add functional variant annotation to MAF file☆11Nov 20, 2024Updated last year
- Identifying large scale inversions between two genomes by mapping genome 1's unique kmers onto genome 2.☆10Jun 6, 2025Updated 8 months ago
- Toolkit for calling structural variants using short or long reads☆115Updated this week
- An efficient index for the colored, compacted, de Bruijn graph☆111Oct 7, 2024Updated last year
- Simulate mutations in genomes☆15Jun 15, 2020Updated 5 years ago
- ✏️ Genome assembly polishing & SNV detection☆72Oct 3, 2025Updated 4 months ago
- Long read aligner☆114May 26, 2023Updated 2 years ago
- Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly☆529Sep 27, 2023Updated 2 years ago
- base-level dotplots from PAF alignments☆31Sep 18, 2025Updated 4 months ago
- for visual evaluation of read support for structural variation☆56Jun 4, 2024Updated last year
- don't get DUP'ed or DEL'ed by your putative SVs.☆107Dec 14, 2020Updated 5 years ago
- R package and wrapper functions for identifying serial structural variations from genome assemblies☆29Sep 21, 2024Updated last year
- Bonsai: Fast, flexible taxonomic analysis and classification☆70Apr 9, 2024Updated last year
- De novo genome assembler.☆11Jul 30, 2018Updated 7 years ago
- QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organisms to Advance Comparative Genomics☆16Jan 12, 2026Updated last month
- Plot structural variant signals from many BAMs and CRAMs☆558Jul 13, 2024Updated last year
- Variant call adjudication☆16Jun 13, 2024Updated last year