A Tool for integrated Quality Control and Preprocessing on FASTQ or BAM/CRAM files
☆114Mar 28, 2024Updated last year
Alternatives and similar repositories for SOAPnuke
Users that are interested in SOAPnuke are comparing it to the libraries listed below
Sorting:
- a lightweight bam file depth statistical tool☆161Sep 13, 2024Updated last year
- Next generation sequencing reads de novo assembler.☆239Sep 20, 2025Updated 6 months ago
- Source code and binaries for the SOAP2 alignment tool developed by BGI.☆10Dec 22, 2023Updated 2 years ago
- BAMixChecker: A fast and efficient tool for sample matching checkup☆15Jun 12, 2022Updated 3 years ago
- Fast and accurately polish the genome generated by long reads.☆240Jan 9, 2025Updated last year
- Reads simulator☆282Sep 3, 2021Updated 4 years ago
- Generate duplex/single consensus reads to reduce sequencing noises and remove duplications☆127Oct 27, 2023Updated 2 years ago
- microsatellite instability detection using tumor only or paired tumor-normal data☆132Jan 6, 2021Updated 5 years ago
- lumpy: a general probabilistic framework for structural variant discovery☆339Feb 22, 2026Updated last month
- A pipeline to de novo assemble the stLFR reads using Supernova Assembler☆20Feb 22, 2023Updated 3 years ago
- ThermoFisher Ion Torrent plugin to detect fetal trisomies and estimate fetal fraction☆17Mar 23, 2018Updated 7 years ago
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆507Feb 26, 2026Updated 3 weeks ago
- Fast and accurate de novo assembler for long reads☆400May 10, 2024Updated last year
- Detect key Units in mosaic Tandem Repeats from representative reads from the same locus☆10Aug 2, 2023Updated 2 years ago
- The next version of bwa-mem☆824Oct 15, 2025Updated 5 months ago
- Pipeline for analyzing rare mutations in metagenome-assembled genomes☆10Apr 4, 2025Updated 11 months ago
- BamDeal: a comprehensive toolkit for bam manipulation☆54Dec 21, 2022Updated 3 years ago
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,303Updated this week
- Mummer alignment tool☆551Feb 4, 2025Updated last year
- Short reads aligner for NIPT/CNV☆16Oct 10, 2018Updated 7 years ago
- MGI sequence platform data multiplexing tool☆12Sep 11, 2019Updated 6 years ago
- Microsatellite instability (MSI) detection for tumor only data.☆114Apr 23, 2024Updated last year
- A gap-closing software tool that uses long reads to enhance genome assembly.☆233Sep 6, 2024Updated last year
- SANEFALCON (Single reAds Nucleosome-basEd FetAL fraCtiON): Calculating the fetal fraction for noninvasive prenatal testing based on genom…☆14Jun 5, 2020Updated 5 years ago
- Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data☆213May 14, 2020Updated 5 years ago
- source code for EVM☆122Nov 29, 2024Updated last year
- samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.☆238Aug 11, 2021Updated 4 years ago
- FxTools: a comprehensive toolkit for FASTA and FASTQ file manipulation☆31Feb 16, 2022Updated 4 years ago
- Gene fusion detection and visualization☆131Feb 21, 2022Updated 4 years ago
- Whole genome workflows☆13Nov 9, 2024Updated last year
- A scaffold assembling pipeline for stLFR reads.☆14Mar 15, 2021Updated 5 years ago
- A Toolkit for analyzing next-generation DNA Re-Sequencing data☆84Feb 15, 2022Updated 4 years ago
- ☆36Mar 16, 2021Updated 5 years ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,143Feb 13, 2026Updated last month
- A tool to root phylogenies☆23Sep 5, 2024Updated last year
- Tools for working with SAM/BAM data☆606Dec 22, 2024Updated last year
- Strelka2 germline and somatic small variant caller☆391Dec 29, 2021Updated 4 years ago
- A single molecule sequence assembler for genomes large and small.☆699Feb 24, 2026Updated 3 weeks ago
- ☆32Dec 6, 2017Updated 8 years ago