ncbi/BAMscale

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ncbi/BAMscale

ncbi

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BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy visualization of commonly used DNA-seq capture based methods.

sra-tools

GeneGPT

Code and data for GeneGPT.

datasets

NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.

Jupyter Notebook

pgap

NCBI Prokaryotic Genome Annotation Pipeline

Common Workflow Language

amr

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

PubReader

A new way to view journal articles

icn3d

web-based protein structure viewer and analysis tool interactively or in batch mode

TPMCalculator

TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files

MedCPT

Code for MedCPT, a model for zero-shot biomedical information retrieval.

dbsnp

Jupyter Notebook

ngs

NGS Language Bindings

SKESA

SKESA assembler

blast_plus_docs

ngs-tools

vadr

Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation

fcs

Foreign Contamination Screening caller scripts and documentation

ncbi-vdb

gprobe

client app for the gRPC health-checking protocol

robotframework-pageobjects

Implementation of the Page Object pattern with Robot Framework and selenium. Also facilitates page object pattern independent of Robot Framework

SSDraw

Jupyter Notebook

clinvar

ClinVar aggregates information about genomic variation and its relationship to human health. Contact us at '[email protected]' with any questions or comments.

rapt

Read Assembly and Annotation Pipeline Tool

ncbi-cxx-toolkit-public

NCBI C++ Toolkit package sources

JATSPreviewStylesheets

JATS Preview Stylesheets

docker

sra-human-scrubber

An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and outputs the edited (cleaned) fastq file that can safely be used for SRA submission.

elastic-blast

ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective

BioConceptVec

Jupyter Notebook

dbvar

AIONER

magicblast

JUDI

This repository contains the source code of JUDI, a workflow management system for developing complex bioinformatics software with many parameter settings. Bioinformatics pipeline: Just Do It!

sratoolkit

SRAToolkit has been REPLACED - see README

bert_gt

egapx

Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation

osiris

OSIRIS is a public domain quality assurance software package that facilitates the assessment of multiplex short tandem repeat (STR) DNA profiles based on laboratory-specific protocols. OSIRIS evaluates the raw electrophoresis data contained in .fsa or .hid files using an independently derived mathematically-based sizing algorithm. OSIRIS currently supports ABI capillary analytical platforms and numerous commercially available marker kits including all CODIS-compliant kits as well as those favored by biomedical laboratories.

pm4ngs

Project Manager for NGS data analysis

BioREx

cwl-ngs-workflows-cbb

A set of CWL tools and workflows used by NCBI Computational Biology Branch for NGS data analysis

Common Workflow Language

consul-announcer

Service announcer for Consul (https://www.consul.io/).

scPopCorn

A python tool to do comparative analysis of mulitple single cell datasets.

Jupyter Notebook

workshop-ncbi-data-with-python

BioRED

cxx-toolkit

EvoGeneX

This repository contains the source code of the R package for EvoGeneX, a software to infer the mode of evolution from the gene expression data.

tree-tool

Incremental building of phylogenetic distance trees

GNorm2

pipelines

Common Workflow Language

tmVar3

graf

Genetic Relationship And Fingerprinting

ribovore

biomedical-citation-selector

PMCXMLConverters

PMC XML Converters

gaptools

dbGaP data validation tool repo

AF2_benchmark

Jupyter Notebook

sars2variantcalling

The NCBI SARS-CoV-2 Variant Calling (SC2VC) Pipeline allows calling high-confidence variants from SARS-CoV-2 NGS data in a standardized format

ICITY

fcs-gx

Foreign Contamination Screening - GX source code

blast-cloud

Documentation for NCBI BLAST AMI

RepairSig

finagle-consul

Service discovery for Finagle cluster with Consul.

NetREX

python-libpq-dev

packit

Python packaging in declarative way (wrapping pbr to make it flexible)

workshop-asm-ngs-2022

Pre-conference workshop for ASM NGS 2022

elastic-blast-demos

ElasticBLAST demos

Jupyter Notebook

PSSS-Bytes2Biology

Petabyte Scale Sequence Search Initiative

HYDROID

Python package for analyzing hydroxyl-radical footprinting experiments of DNA-protein complexes

ncbi-drs

GA4GH DRS Service

ncbi-logging

Log monitoring and gathering infrastructure to feed analytics

cwl-demos

CWL demonstration pipelines

Common Workflow Language

SpeciesAssignment

SpeciesAssignment

niso-jats

dual_fold_coevolution

mti

NLM Medical Text Indexer (MTI)

DbGaP-FHIR-API-Docs

The documentation repository for the dbGaP FHIR API.

Jupyter Notebook

mtix

ML based NLM Medical Text Indexer

ITSx

Not the official ITSx repository, please visit https://microbiology.se/software/itsx/

deeplensnet

gtax

biomedical-citation-selector-trainer

Biomedical Citation Selector Trainer

SuPER

Co-SELECT

This repository contains the source code of Co-SELECT, a computational tool to analyze the results of in vitro HT-SELEX experiments for TF-DNA binding to show the role of DNA shape in TF-DNA binding by using a novel method of deconvoluting the contributions of DNA sequence and DNA shape on the binding.

AceView

Acedb object oriented database engine and AceView/MAGIC RNA_seq pipeline, NCBI/NLM/NIH

stxtyper

StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.

ncbi-xmlwrapp

NCBI’s fork of “xmlwrapp” -- a C++ wrapper for libxml2/libxslt libraries

ncbi-cxx-toolkit-conan

NCBI C++ Toolkit package recipe

biocreative_litcovid

Evaluation scripts of the Biocreative LitCovid track

NETPHIX

A computational tool to identify mutated subnetworks that are associated with a continuous cancer phenotype

SRPRISM

deflake

deflake.py Helps debug a non determinate test (or any flaky program) by running it until it exits with a non-zero exit code.

ncbi_doc_template

Solr-Plugins

Assorted plugins for Solr

ncbi_css_standards

datadicer

GeneSigNet

nlm-dtd

CoV-Dist

cloud-transcriptome-annotation

Time and cost comparison on GCP and AWS for transcriptome annotation

Jupyter Notebook

elastic-blast-docs

ElasticBLAST documentation