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Search results for bioinformatics sequencing
bioinformatics
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sequencing
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169 search results found
Polyrad
⭐
22
Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝
Basic
⭐
21
Gff3toembl
⭐
20
Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
Samql
⭐
20
SQL-like query language for the SAM/BAM file format
Samstat
⭐
20
SAMStat displays various properties of next-generation sequencing reads stored in SAM/BAM format.
Helmsman
⭐
19
highly-efficient & lightweight mutation signature matrix aggregation
Seqmaker.jl
⭐
19
(No maintenance) Next Generation Sequencing Simulation with SNP, Variation and Sequencing Error Integrated
Mageri
⭐
19
MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers
Immunedb
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19
ImmuneDB - A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data
Catt
⭐
18
An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data.
Gatk4_best_practice
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18
GATK4 Best Practice Nextflow Pipeline
Piquant
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18
A pipeline to assess the quantification of transcripts.
Ngcgh
⭐
17
Tools for producing pseudo-cgh of next-generation sequencing data
Taeper
⭐
16
A small python program to simulate a real-time Nanopore sequencing run based on a previous experiment.
Bioutils
⭐
16
provides common tools and lookup tables used primarily by the hgvs and uta packages
Plasmidtron
⭐
16
Assembling the cause of phenotypes and genotypes from NGS data
Vargeno
⭐
15
Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.
Bio Tradis
⭐
15
A set of tools to analyse the output from TraDIS analyses
Sc2 Illumina Pipeline
⭐
14
Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub
Seroba
⭐
14
k-mer based Pipeline to identify the Serotype from Illumina NGS reads
Saffrontree
⭐
14
SaffronTree: Reference free rapid phylogenetic tree construction from raw read data
Mlst_check
⭐
14
Multilocus sequence typing by blast using the schemes from PubMLST
Npreader
⭐
14
Read nanopore sequence reads in real-time
Nanorepeat
⭐
13
NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data
Prophage_tracer
⭐
13
Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment
Chronqc
⭐
13
Manuscript describing ChronQC is now available online in Bioinformatics
Seave
⭐
12
Seave is a web platform that enables genetic variants to be easily filtered and annotated with in silico pathogenicity prediction scores and annotations from popular disease databases. Seave stores genomic variation of all types and sizes, and allows filtering for specific inheritance patterns, quality values, allele frequencies and gene lists. Seave is open source and deployable locally, or on a cloud computing provider, and works readily with gene panel, exome and whole genome data, scaling fr
Kgp
⭐
12
1000 Genomes Project Metadata R Package
Ngs Pipeline
⭐
12
Pipeline for Somatic Variant Calling with WES and WGS data
Pyseqarray
⭐
12
PySeqArray: data manipulation of whole-genome sequencing variants with SeqArray files in Python (pre-release version)
Lodestone
⭐
11
Mycobacterial pipeline
Dendro
⭐
11
Genetic Heterogeneity Profiling by Single Cell RNA Sequencing
Anyvar
⭐
11
[in development] Proof-of-Concept variation translation, validation, and registration service
Deepvariant On Spark
⭐
11
DeepVariant-on-Spark is a germline short variant calling pipeline that runs Google DeepVariant on Apache Spark at scale.
Hyb
⭐
11
hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data
Antler
⭐
10
R package for single-cell RNA-sequencing analysis
Cpg_me
⭐
10
A whole genome bisulfite sequencing (WGBS) pipeline for the alignment and QC of DNA methylation that goes from from raw reads (FastQ) to a CpG count matrix (Bismark cytosine reports)
Readdatastores.jl
⭐
10
Datastores for reads, not your papa's FASTQ files.
Nasqar
⭐
10
NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization
Tostadas
⭐
10
🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
Ngsderive
⭐
10
Forensic analysis tool useful in backwards computing information from next-generation sequencing data.
Kipes
⭐
9
Knowledge-based Identification of Pathway Enzymes (KIPEs) performs an automatic annotation of the flavonoid biosynthesis steps in a new transcriptome of genome sequence assembly.
Seekdeep
⭐
9
Bioinformatic Tools for analyzing targeted amplicon sequencing developed by Nicholas Hathaway of Bailey Lab
Monica
⭐
9
MinION Open Nucleotide Identifier for Continuous Analysis - an open source pathogen identifier for real-time analysis on MinION output
16s Rdna V3 V4
⭐
8
16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/
Toast2018
⭐
7
Introduction to Nanopore Sequencing - Prac material and presentations from The Omics Australia Tutorials Sydney (TOAST) workshop 19th - 20th of March 2018.
Htsinfer
⭐
7
HTSinfer infers metadata from Illumina high throughput sequencing (HTS) data
Ld Pgta
⭐
7
Linkage disequlibrium-informed PGT-A (LD-PGTA). A package for detecting genotypic signatures of aneuploidy from extremely low-coverage sequence data.
Ruby Htslib
⭐
7
HTSlib bindings for Ruby
Cyclobranch
⭐
7
A tool for mass spectrometry data analysis.
Albatradis
⭐
7
Comparative TraDIS analysis
Nanometa_live
⭐
7
A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineered for precision, speed, and user-friendliness, with offline functionality post-initialization.
16smart
⭐
7
16s rRNA Sequencing Meta-analysis Reproducibility Tool (using mothur).
Bioinformatics Figures
⭐
7
Collection of scripts and examples to visualize bioinformatics data
Fonda
⭐
7
Fonda is a framework which offers scalable and automatic analysis of multiple NGS sequencing data types
Harpy
⭐
6
Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included.
Shell_intro_for_bioinformatics_stg
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6
Intro to Shell for Bioinformatics - with STG examples
Cg Pipeline
⭐
6
Genome assembly/prediction/annotation pipeline for the Linux command line
Gbsapp
⭐
5
Automated Pipeline for Variant/Haplotype Calling and Filtering
Seqcode
⭐
5
Suite of command-line software for high-performance graphical analysis of ChIP-seq/RNA-seq/ATAC-seq data
Sib_longreadsworkshop_zurich18
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5
Course material "Bioinformatics of Long Read Sequencing", edition Zürich 2018
Phd Thesis
⭐
5
My PhD thesis - "Tools and techniques for single-cell RNA sequencing data"
Fastq To Bam
⭐
5
Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi
Dajin
⭐
5
One-step genotyping software using a long-read sequencer
Appliedgenomics2020
⭐
5
Description Materials for Spring 2020 Applied Genomics Course
Nanoflow
⭐
5
Bioinformatics pipeline for nanopore sequencing data
Genbankpy
⭐
5
Tools to download, parse and filter GenBank files
Decontaminer
⭐
5
DecontaMiner is a tool designed and developed to investigate the presence of contaminating sequences in unmapped NGS data. It can suggest the presence of contaminating organisms in sequenced samples, that might derive either from laboratory contamination or from their biological source, and in both cases can be considered as worthy of further investigation and experimental validation. The novelty of DecontaMiner is mainly represented by its easy integration with the standard procedures of NGS da
Shiny K Mers
⭐
5
An R package and Shiny app for interactively fitting population parameters to k-mer spectra of diploids, triploids, and tetraploids (allo and auto)
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