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ref_vcf_builder

A little bit of BASH to create a single standard reference VCF from several smaller ones.

rkmh

Classify sequencing reads using MinHash.

rkmh2

Fast read filtering using MinHash

rkmh_paper_response

Code for running simulations for the RKMH paper review response

rkmh_sim_data

Example simulated data for rkmh (viral coinfection analysis using a MinHash toolkit)

rnaseq_tutorial_v1

Archive of original RNAseq.wiki tutorial that accompanied PLoS Comp Bio paper

rov-spec

A pROVenance file format for data lineage (and universal computability)

saas

Build your own SaaS business with SaaS boilerplate. Productive stack: React, Material-UI, Next, MobX, WebSockets, Express, Node, Mongoose, MongoDB. Written with TypeScript.

sdsl-lite

Succinct Data Structure Library 2.0

seqlib

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

seqmini

C++ code for creating minimizer indices on arbitrary FASTA / GFA

seqwish

alignment to variation graph inducer

sga

de novo sequence assembler using string graphs

shimmer

Shimmer is a software package for the characterization of genetic differences between two very similar samples, e.g., a tumor sample and its matched normal tissue sample.

sigan

sigan

sigma

Mutational signature analysis for low statistics SNV data

signatureanalyzer-gpu

SignatureAnalyzer-GPU provides a Tensorflow implementation of automatic relevance determination non-negative matrix factorization (ARD NMF).

sigprofilerextractor

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

sigprofilerhelper

Helper scripts for the SigProfiler suite of mutational signature analysis tools

sigprofilermatrixgenerator

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.

sigprofilerplotting

SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.

siminf

Simulate coinfections of viral strains

simple_mutator

A script for introducing mutations in a reference genome at specific rates.

simplegpuhashtable

A simple GPU hash table implemented in CUDA using lock free techniques

single_file_libs

List of single-file C/C++ libraries.

sketch

C++ Implementations of sketch data structures with SIMD Parallelism, including Python bindings

smithwaterman

smith-waterman-gotoh alignment algorithm

smoothxg

linearize and simplify variation graphs using blocked partial order alignment

smoove

structural variant calling and genotyping with existing tools, but, smoothly.

smurf