jessicakan789

octopus

Bayesian haplotype-based mutation calling

MIP

Mutation Identification Pipeline. Read the latest documentation:

NextFlow_RD_Genomic

training

Nextflow training material

VEP_plugins

Plugins for the Ensembl Variant Effect Predictor (VEP)

Alternative-Splicing-Tools

A list of alternative splicing analysis resources

2023-Software-Development-Assessment

giab_data_indexes

This repository contains data indexes from NIST's Genome in a Bottle project.

benchmarking-tools

Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls

cnv-depth-of-coverage-comparison

Intro-to-programming-unit3-CPD

materials to share with staff

dx-streaming-upload

The DNAnexus incremental upload script packaged as an Ansible Role

eggd_tso500

Runs the Illumina TSO500 local analysis app.

seglh-naming

SEGLH naming schemes

bioinformatics

:microscope: Path to a free self-taught education in Bioinformatics!

STPresources

mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

svcurator

svviz

Read visualizer for structural variants

samplot

Plot structural variant signals from many BAMs and CRAMs

vcf-validator

Validation suite for Variant Call Format (VCF) files, implemented using C++11

cfg-homework-template

A template for how to structure homework submissions

vcftools

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

public-apis

A collective list of free APIs

Picky

Structural Variants Pipeline for Long Reads

cuteSV

Long read based human genomic structural variation detection with cuteSV

Sniffles

Structural variation caller using third generation sequencing

nanopolish

Signal-level algorithms for MinION data

nanofilt

Filtering and trimming of long read sequencing data

pycoQC

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)