LoFreq Star: Sensitive variant calling from sequencing data
☆111Oct 16, 2025Updated 5 months ago
Alternatives and similar repositories for lofreq
Users that are interested in lofreq are comparing it to the libraries listed below
Sorting:
- LoFreq Version 3☆27Feb 25, 2021Updated 5 years ago
- Repo for the software suite ShoRAH (Short Reads Assembly into Haplotypes)☆41Feb 24, 2023Updated 3 years ago
- Bayesian haplotype-based mutation calling☆323Feb 13, 2026Updated last month
- Microassembly based somatic variant caller for NGS data☆154Jun 23, 2022Updated 3 years ago
- use the noise☆15Apr 15, 2020Updated 5 years ago
- URMAP ultra-fast read mapper☆38Jun 15, 2020Updated 5 years ago
- Detects human contamination in bam files☆16Sep 10, 2020Updated 5 years ago
- Indel-aware consensus for aligned BAM☆21Aug 16, 2025Updated 7 months ago
- Concordance and contamination estimator for tumor–normal pairs☆59Oct 22, 2024Updated last year
- A wrapper for calling small variants from human germline high-coverage single-sample Illumina data☆14Jul 21, 2019Updated 6 years ago
- Simplify snpEff annotations for interesting cases☆22Feb 18, 2019Updated 7 years ago
- seqcover allows users to view coverage for hundreds of genes and dozens of samples☆52Apr 9, 2021Updated 4 years ago
- don't get DUP'ed or DEL'ed by your putative SVs.☆107Dec 14, 2020Updated 5 years ago
- Read visualizer for structural variants☆84Aug 18, 2018Updated 7 years ago
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆507Feb 26, 2026Updated 3 weeks ago
- annotate a VCF with other VCFs/BEDs/tabixed files☆398Aug 30, 2025Updated 6 months ago
- Computational Framework to reconstructing tumor clone structures☆15Mar 31, 2021Updated 4 years ago
- tools for adding mutations to existing .bam files, used for testing mutation callers☆247Oct 18, 2024Updated last year
- Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer☆21Dec 8, 2020Updated 5 years ago
- ABRA2☆95Dec 2, 2022Updated 3 years ago
- The next version of bwa-mem☆823Oct 15, 2025Updated 5 months ago
- find large indels (in the blind spot between GATK/freebayes and SV callers)☆39Dec 3, 2017Updated 8 years ago
- goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary☆225Sep 18, 2025Updated 6 months ago
- A tool set for short variant discovery in genetic sequence data.☆204May 4, 2021Updated 4 years ago
- VILOCA: VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data☆23Oct 21, 2025Updated 4 months ago
- Computes a consensus sequence with wobbles, ambiguous bases, and in-frame insertions, from a NGS read alignment.☆18May 14, 2018Updated 7 years ago
- base-accurate DNA sequence alignments using edlib and mashmap2☆32Feb 15, 2021Updated 5 years ago
- Smart VCF parser DSL☆83May 24, 2022Updated 3 years ago
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Aug 4, 2021Updated 4 years ago
- VarDict☆202Jan 5, 2024Updated 2 years ago
- structural variant calling and genotyping with existing tools, but, smoothly.☆264Jun 17, 2024Updated last year
- a lightweight db framework for exploring genetic variation.☆326Apr 28, 2020Updated 5 years ago
- De Bruijn graph construction for large k.☆17Aug 31, 2021Updated 4 years ago
- Generate interactive dotplot from mummer4 output using plotly☆27Feb 29, 2020Updated 6 years ago
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆25Feb 17, 2023Updated 3 years ago
- ViromeScan allows the user to explore and taxonomically characterize the virome from metagenomic reads, efficiently denoising samples fro…☆13Feb 13, 2023Updated 3 years ago
- Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data☆121Aug 21, 2023Updated 2 years ago
- A wrapper to Heng Li's kseq/readfq, an efficient FastQ/Fasta parser☆15Jun 28, 2023Updated 2 years ago
- Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata☆58Feb 17, 2022Updated 4 years ago