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breakseq2

BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants

bwa

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences

daedalus

ectmb

fermi-lite

Standalone C library for assembling Illumina short reads in small regions

huref-gs

ichorcna

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

idp

IDP is a statistical isoform prediction method to construct possible isoform candidates from the union of long reads and short reads with spliced alignment

longislnd

LongISLND - Long In silico Sequencing of Lengthy and Noisy Datatypes

lsc

LSC is a long read error correction tool. It offers fast correction with high sensitivity and good accuracy.

metasv

MetaSV: An accurate and integrative structural-variant caller for next generation sequencing

neusomatic

NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection

pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

qbc_single_cell_analysis_ngs

rnacocktail

seqlib

C++ htslib/bwa-mem/fermi interface for interrogating sequence data

somaticseq

An ensemble approach to accurately detect somatic mutations using SomaticSeq

swifr

varsim

VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications