An efficient FASTQ manipulation suite
☆139Jan 27, 2020Updated 6 years ago
Alternatives and similar repositories for fqtools
Users that are interested in fqtools are comparing it to the libraries listed below
Sorting:
- AlignerBoost is a generalized software toolkit for boosting Next-Gen sequencing mapping precision using a Bayesian based mapping quality …☆11Mar 1, 2022Updated 4 years ago
- Classify sequencing reads using MinHash.☆48Apr 6, 2020Updated 5 years ago
- Match up paired end fastq files quickly and efficiently.☆155Jun 2, 2024Updated last year
- goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary☆225Sep 18, 2025Updated 5 months ago
- C++ htslib/bwa-mem/fermi interface for interrogating sequence data☆138Sep 16, 2025Updated 5 months ago
- Bayesian haplotype-based mutation calling☆323Feb 13, 2026Updated 3 weeks ago
- annotate a VCF with other VCFs/BEDs/tabixed files☆398Aug 30, 2025Updated 6 months ago
- A tool to reduce the size of Oxford Nanopore Technologies' datasets without losing information☆30Dec 13, 2023Updated 2 years ago
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆143Aug 24, 2025Updated 6 months ago
- Flexible genotype query among 30,000+ samples whole-genome☆94Sep 4, 2019Updated 6 years ago
- ☆96Sep 21, 2022Updated 3 years ago
- seqcover allows users to view coverage for hundreds of genes and dozens of samples☆52Apr 9, 2021Updated 4 years ago
- Scaffolding of genomic assemblies with RNA seq data☆15Oct 8, 2015Updated 10 years ago
- Filtering and profiling of next-generational sequencing data using region-specific rules☆79Oct 30, 2023Updated 2 years ago
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆463Dec 26, 2024Updated last year
- a wee tool for random access into BGZF files.☆86May 10, 2018Updated 7 years ago
- DNA kmer operations for nim☆14Apr 24, 2022Updated 3 years ago
- Symmetric DUST for finding low-complexity regions in DNA sequences☆45Jul 24, 2025Updated 7 months ago
- Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.☆24Jan 9, 2021Updated 5 years ago
- Code to create a PRG from a Multiple Sequence Alignment file☆25Sep 10, 2025Updated 5 months ago
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆828Feb 10, 2026Updated 3 weeks ago
- Ultrafast de novo assembly for long noisy reads (though having no consensus step)☆352Jul 19, 2025Updated 7 months ago
- samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.☆238Aug 11, 2021Updated 4 years ago
- Nanopore read de-multiplexer☆13Mar 25, 2020Updated 5 years ago
- Parallel Sequence to Graph Alignment☆36Nov 26, 2022Updated 3 years ago
- High-performance error correction for Illumina resequencing data☆74May 31, 2016Updated 9 years ago
- A tool set for short variant discovery in genetic sequence data.☆204May 4, 2021Updated 4 years ago
- Yet another k-mer analyzer☆161Dec 30, 2025Updated 2 months ago
- de novo targeted gene assembly☆22Apr 16, 2021Updated 4 years ago
- LoFreq Star: Sensitive variant calling from sequencing data☆110Oct 16, 2025Updated 4 months ago
- Text Only Genome Viewer!☆233Updated this week
- ☆15Aug 14, 2020Updated 5 years ago
- Mostly deprecated in favor of : https://github.com/hbc/bcbioRNASeq. Quality control, differential gene/transcript expression and pathway …☆25Dec 11, 2017Updated 8 years ago
- Java utilities for Bioinformatics☆518Feb 6, 2026Updated last month
- The D4 Quantitative Data Format☆169Nov 28, 2025Updated 3 months ago
- A deletion finder through re-aligning the whole soft-clipping read☆12Jul 2, 2016Updated 9 years ago
- Rapid sensitive and accurate read mapping via quasi-mapping☆90Jun 5, 2020Updated 5 years ago
- Tools for bam file processing☆55Apr 20, 2015Updated 10 years ago
- VCF-kit: Assorted utilities for the variant call format☆133Jul 10, 2025Updated 7 months ago