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adtex

Aberration Detection in Tumour Exome

ascat

ASCAT copy number R package

bafplot

calculate BAF and plot BAF fig to assist the estimation the tumor purity and ploidy visually

basevar

This is the official development repository for BaseVar, which call variants for ultra low-pass (<1.0x) WGS data, especially for NIPT data

bds-files

Supplementary files for my book, "Bioinformatics Data Skills"

bioinfo_algorithm_collections

re-write classical bioinfo algorithms, such as simth-waterman local alignment, HMM, BWT, PCA et.al

breakdancer

SV detection from paired end reads mapping

clustalo_2019ncov

ClustalO_2019nCoV plugin for Ion Torrent S5 Sequencing Platform

cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing

cnvkit

Copy number variant detection from targeted DNA sequencing

codex2

Full-spectrum copy number variation detection by high-throughput DNA sequencing

convading

Copy Number Variation Detection In Next-generation sequencing Gene panels was designed for small (single-exon) copy number variation (CNV) detection in high coverage next-generation sequencing (NGS) data

ctdna_wgs_cnv

papers calling CNV from ctDNA WGS data

defuse

An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

devtools

Tools to make an R developer's life easier

ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

facets

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

fastqcreator

fastv

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.

flt3_itd_pindel

detect FLT3-internal tandem duplication using Pindel

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

freec

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data

fsz_substr_finding_problem

find all positions of a query string in a long sequence using exact matching

geexcnv

analysis germline CNV (exon-level and gene-level) from capture data

genefuse

Gene fusion detection and visualization

gisaid_2019ncov_mut_freq

hfphp

hifitongs