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Search results for java sequencing
java
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sequencing
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42 search results found
Adam
⭐
966
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
Picard
⭐
914
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Fastqc
⭐
362
A quality control analysis tool for high throughput sequencing data
Htsjdk
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271
A Java API for high-throughput sequencing data (HTS) formats.
Miso Lims
⭐
214
MISO: An open-source LIMS for NGS sequencing centres
Artemis
⭐
191
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
Dnanalyzer
⭐
122
Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools
Hmmratac
⭐
49
HMMRATAC peak caller for ATAC-seq data
Issho
⭐
46
A standalone sequencer for grid-based devices.
Rtg Core
⭐
41
RTG Core: Software for alignment and analysis of next-gen sequencing data.
Ngsepcore
⭐
40
NGSEP is an integrated framework for analysis of high throughput sequencing (HTS) reads. The main functionality of NGSEP is the variants detector, which allows to make integrated discovery and genotyping of Single Nucleotide Variants (SNVs), insertions, deletions, and genomic regions with copy number variation (CNVs).
Pathos
⭐
22
PathOS is a clinical application for filtering, analysing and reporting on NGS variants
Japsa
⭐
19
Just Another JAva Package for Sequence Analysis
Mageri
⭐
19
MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers
Upgrade Framework
⭐
17
A product-agnostic framework for defining and sequencing upgrades
Ngs
⭐
17
Next generation sequencing (NGS/HTS) tools.
Goby
⭐
17
Goby framework and tools for analysis of high-throughput sequencing data
Useq
⭐
17
180+ Java applications for analyzing next generation sequencing data from ChIPSeq, RNASeq, BisSeq, DNASeq, variant annotation/ filtering, alignment/VCF QC, capture array design, IGV/ DAS2/IGB/UCSC file manipulation, etc. Both GUI and cmd line interfaces.
Java Genomics Toolkit
⭐
16
Collection of scripts for working with Wiggle files and analyzing sequencing data
Snpsvm
⭐
15
A support vector machine for calling variants from next-gen sequencing data
Gbsx
⭐
14
GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments
Tiger
⭐
13
Toolkits Integrated for Genetic and Evolutionary Research
Hadoopcnv
⭐
12
HadoopCNV is a MapReduce-based copy number variation caller for genome sequencing data
Seal
⭐
11
SEquence ALignment evaluation suite
Gnomex
⭐
11
A genomic LIMS and data repository.
Kggseq
⭐
11
Seqbuster
⭐
10
pipeline for the analysis of small RNA data
Seqpig
⭐
9
SeqPig is a library for Apache Pig for the distributed analysis of large sequencing datasets. It provides import and export functions for file formats commonly used for sequencing data, as well as a collection of Pig user-defined-functions (UDF’s) to help process aligned and unaligned sequence data.
F5n
⭐
8
Genopo a.k.a. F5N - A nanopore sequencing analysis toolkit for Android smartphones https://nanoporetech.com
Fonda
⭐
7
Fonda is a framework which offers scalable and automatic analysis of multiple NGS sequencing data types
Biocode Lims
⭐
7
The Biocode LIMS plugin integrates Geneious with your lab workflow, allowing you to track processes through tissue sample, extraction, PCR, sequencing and assembly. It is best suited for large scale DNA barcoding efforts.
Quasirecomb
⭐
7
Probabilistic inference of viral quasispecies subject to recombination (viral haplotype reconstruction).
Multibreak Sv
⭐
7
MultiBreak-SV identifies structural variants from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.
Cod
⭐
7
It's all about Cost of Delay. Currently this application can help you visualizing the effects on cost of delay for different sequencing of projects.
Convector
⭐
6
CONVector tool for exon-scale CNV detection in target massively parallel sequencing (MPS) data.
Seqcode Core
⭐
6
SeqCode: Java code for the analysis of high-throughput sequencing data
Openga
⭐
5
This OpenGA aims at solving different kinds of problems, including continuous, discrete, or sequencing problems. In addition, these problems may accompany with multiple objective problems. OpenGA is able to solve them because this library adopts many evolutionary strategies.
Multigps Archive
⭐
5
SeqCode: Java code for the analysis of high-throughput sequencing data
Harold
⭐
5
Haplotype Reconstruction of Longitudinal Deep sequencing data
Denovogui
⭐
5
Graphical user interface for de novo sequencing of tandem mass spectra
Discvr
⭐
5
A Viral detection tool from High-Throughput Sequencing (HTS) data
Sugar
⭐
5
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