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purecn

Copy number calling and variant classification using targeted short read sequencing

purityploidyest

estimate tumor purity and ploidy from tumor-only WES/Panel data

pyloh

Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity

pytorch

Tensors and Dynamic neural networks in Python with strong GPU acceleration

readdepth

R package for inferring copy number from read depth

repaq

A fast lossless FASTQ compressor with ultra-high compression ratio

reportsummary_2019ncov

sambamba

Tools for working with SAM/BAM/CRAM data

samclip

Filter SAM file for soft and hard clipped alignments

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

seeksv

A bioinformatics tool for SV detection and virus integration discovery

seqan

SeqAn's official repository.

seqtk

Toolkit for processing sequences in FASTA/Q formats

sgz

simfastq

Simulation fastq files from a given reference genome

simug

simuG: a general-purpose genome simulator

simvar2fastq

Simulate SNV/InDel at a specific genome position to make Fastq files

sjm

Simple Job Manager

splitfusion

detect DNA fusion using split read

ts

Torrent Suite

uniquekmer

Generate unique KMERs for every contig in a FASTA file

vardict

VarDict

visualmsi

Detect and visualize microsatellite instability(MSI) from NGS data

xiaohuaniu0032.github.io

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