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aceseqworkflow

Allele-specific copy number estimation with whole genome sequencing

bamdst

a lightweight bam file depth statistical tool

charger

Characterization of Germline variants

cnaclinic

conpair

Concordance and contamination estimator for tumor–normal pairs

deeppath

Classification of Lung cancer slide images using deep-learning

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

detin

DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.

duplexfiltering

duplex DNA molecule identification tool for ultra-sensitive SNV detection

fishplot

Create timecourse "fish plots" that show changes in the clonal architecture of tumors

hmmcopy_utils

Tools for extracting read counts and gc and mappability statistics in preparation for running HMMCopy.

hrdetect-pipeline

ichorcna

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

lancet

Microassembly based somatic variant caller for NGS data

manta

Structural variant and indel caller for mapped sequencing data

mutationalpatterns

R package for extracting and visualizing mutational patterns in base substitution catalogues

orchid

A novel management, annotation, and machine learning framework for analyzing cancer mutations

proxy_pool

Python爬虫代理IP池(proxy pool)

repaq

repack Illumina format FASTQ to a smaller binary file (.rfq), which can be further compressed by xz (.rfq.xz)

samplot

Plot structural variant signals from many BAMs and CRAMs

scarhrd

sjm

Simple Job Manager

somaticseq

An ensemble approach to accurately detect somatic mutations using SomaticSeq

strelka

Strelka2 germline and somatic small variant caller

superfreq

Analysis pipeline for cancer exomes

tensorflow

Computation using data flow graphs for scalable machine learning

tner

TNER: Tri-Nucleotide Error Reducer for ctDNA detection