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JonathanAbrahams1337

JonathanAbrahams1337

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Metabuli

Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.

Language:C++License:GPL-3.0Stargazers:89Issues:0Issues:0

sylph

ultrafast genome querying and taxonomic profiling for metagenomic samples by abundance-corrected minhash.

Language:RustLicense:MITStargazers:113Issues:0Issues:0

NGS-PrimerPlex

NGS-PrimerPlex is a high-throughput tool for mupltiplex primer design

Language:PythonLicense:GPL-3.0Stargazers:49Issues:0Issues:0

OPAL

OPAL: Open-community Profiling Assessment tooL

Language:PythonLicense:Apache-2.0Stargazers:25Issues:0Issues:0

multiply

Multiplex PCR design, in silico

Language:PythonLicense:MITStargazers:11Issues:0Issues:0

melt

Standalone nucleotide sequence melt temp calculator for Python

Language:PythonLicense:AGPL-3.0Stargazers:7Issues:0Issues:0

SADDLE

Language:Jupyter NotebookStargazers:31Issues:0Issues:0

PCRamp

Software for designing multiplex-compatible, PCR-based enrichment assays

Language:C++License:NOASSERTIONStargazers:5Issues:0Issues:0

Porechop_ABI

Adapter trimmer for Oxford Nanopore reads using ab initio method

Language:C++License:GPL-3.0Stargazers:31Issues:0Issues:0

ska.rust

Split k-mer analysis – version 2

Language:RustLicense:Apache-2.0Stargazers:56Issues:0Issues:0

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Language:PythonLicense:GPL-3.0Stargazers:407Issues:0Issues:0

igv-reports

Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.

Language:PythonLicense:MITStargazers:328Issues:0Issues:0

assembly-stats

Assembly statistic visualisation

Language:JavaScriptLicense:MITStargazers:85Issues:0Issues:0

thermonucleotideBLAST

Searching DNA/RNA sequence databases with PCR and/or probe queries

Language:C++License:NOASSERTIONStargazers:16Issues:0Issues:0

mlst

:id: Scan contig files against PubMLST typing schemes

Language:ShellLicense:GPL-2.0Stargazers:184Issues:0Issues:0

MentaLiST

The MLST pipeline developed by the PathOGiST research group

Language:JuliaLicense:MITStargazers:34Issues:0Issues:0

patterns

A curated collection of Nextflow implementation patterns

Language:NextflowLicense:MITStargazers:316Issues:0Issues:0

genome_collector

:stars: Easily download genomes and build BLAST/Bowtie indexes in Python

Language:PythonLicense:NOASSERTIONStargazers:21Issues:0Issues:0

SpolLineages

Rapid and precise prediction of Mycobacterium tuberculosis complex families

Language:JavaLicense:GPL-3.0Stargazers:6Issues:0Issues:0

GraphMB

Language:PythonLicense:MITStargazers:35Issues:0Issues:0

GTDBTk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Language:PythonLicense:GPL-3.0Stargazers:445Issues:0Issues:0

teaching

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classifier

RDP extensible sequence classifier for fungal lsu, bacterial and archaeal 16s

Language:JavaLicense:GPL-2.0Stargazers:53Issues:0Issues:0

barrnap

:microscope: :leo: Bacterial ribosomal RNA predictor

Language:PerlLicense:GPL-3.0Stargazers:207Issues:0Issues:0

AMBER

AMBER: Assessment of Metagenome BinnERs

Language:PythonLicense:GPL-3.0Stargazers:25Issues:0Issues:0

czid-dag

Please see https://github.com/chanzuckerberg/czid-workflows for the latest version of CZ ID workflows.

Language:PythonLicense:MITStargazers:27Issues:0Issues:0

MetaScope

An R-based approach for preprocessing and aligning 16S, metagenomic, and metatranscriptomic data (PathoScope version 3.0)

Language:RLicense:GPL-3.0Stargazers:12Issues:0Issues:0

MFEprimer-2.0

MFEprimer-2.0: A fast thermodynamics-based program for checking PCR primer specificity

Language:PythonLicense:NOASSERTIONStargazers:36Issues:0Issues:0

ThermoAlign

ThermoAlign: software for automated primer design

Language:PythonLicense:GPL-3.0Stargazers:24Issues:0Issues:0

ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

Language:PythonLicense:Apache-2.0Stargazers:902Issues:0Issues:0