Toolkit for processing TAB-delimited format
☆62Oct 10, 2024Updated last year
Alternatives and similar repositories for tabtk
Users that are interested in tabtk are comparing it to the libraries listed below
Sorting:
- Naive PCA for genotype data☆10Jul 27, 2016Updated 9 years ago
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆143Aug 24, 2025Updated 6 months ago
- add true-negative SVs from a population callset to a truth-set.☆15Jun 17, 2022Updated 3 years ago
- PAF (pairwise alignment format) validator based on extended CIGAR strings☆15Aug 10, 2025Updated 6 months ago
- A filter algorithm with program to filter an alignment or mapping file☆12May 15, 2025Updated 9 months ago
- A pipeline creation tool using Snakemake☆12Feb 20, 2026Updated last week
- Hidden Markov Model based Copy number caller☆20Dec 9, 2025Updated 2 months ago
- Coronavirus (SARS-Cov-2) sequencing analysis☆10Oct 5, 2021Updated 4 years ago
- convert reads from repeated measures of same piece of DNA into spaced matricies for deep learners.☆14Apr 21, 2023Updated 2 years ago
- Optimal distance lower bound k-mer sampling.☆12Jun 19, 2024Updated last year
- quickly filter fastq files by matching sequences to a set of regex patterns☆58Dec 14, 2025Updated 2 months ago
- Lightweight Python interfaces for reading, writing, and querying genomic regions (BED)☆14Nov 25, 2025Updated 3 months ago
- De novo chromosome-level scaffolding and phasing tool using Hi-C☆30Nov 23, 2025Updated 3 months ago
- This tools counts the number of specific k-mers within sequence data. The counts can then be compare to other counts to determine to comp…☆30Nov 25, 2024Updated last year
- De novo assembly based variant calling pipeline for Illumina short reads☆110Nov 30, 2020Updated 5 years ago
- BioDSL (pronounced Biodiesel) is a Domain Specific Language for creating bioinformatic analysis workflows.☆16Jul 30, 2018Updated 7 years ago
- Haplotype phaser for next-generation sequencing data☆13Jan 13, 2022Updated 4 years ago
- Genomic VCF to tab-separated values☆48Mar 9, 2023Updated 2 years ago
- Overlap assembler of paired-end DNA sequences generated by Illumina☆23Sep 2, 2016Updated 9 years ago
- A lightweight Python graphing API for genomic features☆15Jul 8, 2022Updated 3 years ago
- adds sample names and read-group (RG) tags to BAM alignments☆51Dec 14, 2020Updated 5 years ago
- a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads☆211Oct 2, 2025Updated 5 months ago
- A tool set for short variant discovery in genetic sequence data.☆204May 4, 2021Updated 4 years ago
- Tools for working with SAM/BAM data☆605Dec 22, 2024Updated last year
- Exact Tandem Repeat Finder (not a TRF replacement)☆51Oct 22, 2019Updated 6 years ago
- De novo tandem repeat calling from PacBio HiFi data☆19Dec 5, 2025Updated 2 months ago
- RCK: Reconstruction of clone- and haplotype-specific Cancer Karyotypes☆18Apr 2, 2020Updated 5 years ago
- A simple tool to fix PacBio fasta/q that was not properly split into subreads☆16Jun 10, 2021Updated 4 years ago
- BED QC tool (in the making)☆18Aug 19, 2022Updated 3 years ago
- a tool to evaluate long-read error correction mainly with PacBio High-Fidelity Reads (HiFi reads).☆21Dec 5, 2023Updated 2 years ago
- command-line querying+conversion of bigwigs and a nim wrapper for dpryan's libbigwig☆16May 2, 2020Updated 5 years ago
- ☆33Nov 6, 2022Updated 3 years ago
- A Rust library for storing generic genomic data by sorted chromosome name☆17Sep 26, 2024Updated last year
- De Bruijn graph construction for large k.☆17Aug 31, 2021Updated 4 years ago
- Kmer Analysis of Pileups for Genotyping☆36Jan 30, 2026Updated last month
- ☆13May 27, 2025Updated 9 months ago
- Genome-wide TR catalog and variation clusters described in [Weisburd, Dolzhenko, et al. 2024]☆17Feb 19, 2026Updated last week
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Aug 4, 2021Updated 4 years ago
- Variant calling and somatic mutation/CNV detection for next-generation sequencing data☆165Mar 28, 2023Updated 2 years ago