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Search results for sequencing fastq
fastq
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sequencing
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71 search results found
Fastp
⭐
1,602
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging.
Afterqc
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157
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Genomics
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154
A collection of scripts and notes related to genomics and bioinformatics
Seq2science
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132
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
Ngscheckmate
⭐
106
Software program for checking sample matching for NGS data
Seqfu2
⭐
96
🚀 seqfu - Sequece Fastx Utilities
Assembly Stats
⭐
92
Get assembly statistics from FASTA and FASTQ files
Mcclintock
⭐
83
Meta-pipeline to identify transposable element insertions using next generation sequencing data
Neat Genreads
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72
NEAT read simulation tools
Nanostat
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63
Create statistic summary of an Oxford Nanopore read dataset
Opengene.jl
⭐
61
(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia
Fastv
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56
An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.
Pyflow Chipseq
⭐
55
a snakemake pipeline to process ChIP-seq files from GEO or in-house
Poreplex
⭐
51
A versatile sequenced read processor for nanopore direct RNA sequencing
Falco
⭐
50
A C++ drop-in replacement of FastQC to assess the quality of sequence read data
Fastaq
⭐
45
Python3 scripts to manipulate FASTA and FASTQ files
Ngspeciesid
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41
Reference-free clustering and consensus forming of long-read amplicon sequencing
Assembly_improvement
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39
Improve the quality of a denovo assembly by scaffolding and gap filling
Fastq_utils
⭐
29
Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.
Qc3
⭐
27
QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.
Natrix
⭐
21
Open-source bioinformatics pipeline for the preprocessing of raw sequencing data.
Defq
⭐
20
Ultra-fast Multi-threaded FASTQ Demultiplexing
Assembler Components
⭐
20
Components of genome sequence assembly tools
Isaac2
⭐
20
Aligner for sequencing data
Peat
⭐
20
An ultra fast and accurate paired-end adapter trimmer that needs no a priori adapter sequences.
Isaac3
⭐
18
Aligner for sequencing data
Ptrimmer
⭐
17
Used to trim off the primer sequence from mutiplex amplicon sequencing
Dnbelab_c_series_scrna Analysis Software
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16
An open source and flexible pipeline to analyze DNBelab C Series single-cell RNA datasets.
Pheniqs
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16
Fast and accurate sequence demultiplexing
Enasearch
⭐
15
A Python library for interacting with ENA's API
Bio Tradis
⭐
15
A set of tools to analyse the output from TraDIS analyses
Krocus
⭐
14
Predict MLST directly from uncorrected long reads
Fqless
⭐
11
less like viewer for fastq files
Autoadapt
⭐
11
Automatic quality control for FASTQ sequencing files
Imonitor
⭐
11
This script use to analyze the immune repertoire sequenced by high throughtput sequencing
Sequencing_for_genetics
⭐
11
유전학자를 위한 시퀀싱 자료 분석
Libngs
⭐
10
The Nifty GNU Sequence Library
Longread_plots
⭐
10
A collection of plots for long read sequencing FastQ files from devices like Oxford Nanopore's MinION and PromethION.
Bisulfite Seq Tools
⭐
10
Suite of tools to conduct methylation data analysis. Methods from this workspace can be used for alignment and quality control analysis for various protocols including Whole Genom Bisulfite Sequencing (WGBS), Reduced Representation Bisulfite Sequencing (RRBS) and Hybrid Selection Bisulfite Sequencing (HSBS).
Damidseq_pipeline
⭐
10
An automated pipeline for processing DamID sequencing datasets
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)
Nanoget
⭐
10
Functions to extract information from Oxford Nanopore sequencing data and alignments
Larry
⭐
10
Readdatastores.jl
⭐
10
Datastores for reads, not your papa's FASTQ files.
Fast5_fetcher
⭐
9
A tool for fetching nanopore fast5 files after filtering via demultiplexing, alignment, or other, to improve downstream processing efficiency
Pypore
⭐
9
A python tool box for fast and accurate quality control, conversion and alignment of nanopore sequencing data
Seq Collection
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9
Freehic
⭐
8
FreeHi-C pipeline for high fidelity Hi-C data simulation.
Tabsat
⭐
8
Targeted Amplicon Bisulfite Sequencing Analysis Tool
Abi2fastq
⭐
8
abi2fastq is a small utility to convert Sanger sequencing reads in .abi (applied biosystems) format to FASTQ
Cplate
⭐
7
Digestion template-based deconvolution for chromatin structure inference.
Splitaake
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7
demultiplex massively parallel sequencing data
Betaduck
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7
Organising / summarising a PromethION Beta Nanopore Run
Athlon
⭐
7
Accurate Typing of Human Leukocyte Antigen (HLA) by Oxford Nanopore Sequencing
Sip
⭐
7
SIP, a Single-cell Interchangeable Pipeline, still under construction
Fonda
⭐
7
Fonda is a framework which offers scalable and automatic analysis of multiple NGS sequencing data types
Braincode
⭐
7
Script and pipeline for BRAINcode project
Qbrc Somatic Pipeline
⭐
7
QBRC Somatic Mutation Calling Pipeline
Seqkit
⭐
7
Toolkit for manipulating FASTA and SAM files
Nanopore_ncm18
⭐
7
Helpful scripts for working with Oxford Nanopore Sequencing data
Xs
⭐
6
A FASTQ read simulator
Ngs
⭐
6
Next-generation sequencing analysis pipelines & scrips
Fastq Info
⭐
6
Calculate fastq reads and sequencing coverage
Pollux
⭐
6
Error correction of second-generation sequencing technologies.
Getitd
⭐
6
Software for FLT3-ITD detection and MRD monitoring assay
Itsxpress
⭐
6
Software to trim the ITS region of FASTQ sequences for amplicon sequencing analysis
Cypiripi
⭐
5
A tool for finding out the CYP2D6/CYP2D7 genotypes in the HTS reads
Idemux
⭐
5
Idemux is a command line tool designed to demultiplex paired-end fastq files from QuantSeq-Pool.
Barcseek
⭐
5
BarcSeek: A Flexible Barcode Partitioning Tool for Demultiplexing Genomic Sequencing Data
Kodoja
⭐
5
Kodoja: identifying viruses from plant RNA sequencing data
Rdxon
⭐
5
Reference-free FASTQ filter for rare germline and somatic variants
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