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Search results for bioinformatics fastq
bioinformatics
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fastq
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89 search results found
Oneliners
⭐
1,705
Useful bash one-liners for bioinformatics.
Fastp
⭐
1,602
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging.
Seqtk
⭐
1,148
Toolkit for processing sequences in FASTA/Q formats
Seqkit
⭐
1,133
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Bwa Mem2
⭐
645
The next version of bwa-mem
Vsearch
⭐
605
Versatile open-source tool for microbiome analysis
Seqan3
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373
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
Juicer
⭐
313
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Bioinformatics One Liners
⭐
277
Bioinformatics one liners from Ming Tang
Parallel Fastq Dump
⭐
224
parallel fastq-dump wrapper
Pyfastx
⭐
211
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
Afterqc
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157
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Rasusa
⭐
156
Randomly subsample sequencing reads to a specified coverage
Genomics
⭐
154
A collection of scripts and notes related to genomics and bioinformatics
Ngless
⭐
141
NGLess: NGS with less work
Biofast
⭐
132
Benchmarking programming languages/implementations for common tasks in Bioinformatics
Seq2science
⭐
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.
Mutscan
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127
Detect and visualize target mutations by scanning FastQ files directly
Fastqt
⭐
109
FastQC port to Qt5: A quality control tool for high throughput sequence data.
Fqtools
⭐
105
An efficient FASTQ manipulation suite
Readfq
⭐
105
Fast multi-line FASTA/Q reader in several programming languages
Isoquant
⭐
98
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
Seqfu2
⭐
96
🚀 seqfu - Sequece Fastx Utilities
Fastqp
⭐
94
Simple FASTQ quality assessment using Python
Assembly Stats
⭐
92
Get assembly statistics from FASTA and FASTQ files
Cljam
⭐
87
A DNA Sequence Alignment/Map (SAM) library for Clojure
Genefuse
⭐
86
Gene fusion detection and visualization
Fqgrep
⭐
75
Grep for FASTQ files
Celescope
⭐
73
Single Cell Analysis Pipelines
Scatac Pro
⭐
64
A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
Opengene.jl
⭐
61
(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia
Fasten
⭐
57
👷 Fasten toolkit, for streaming operations on fastq files
Fastv
⭐
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.
Fq
⭐
54
Command line utility for manipulating Illumina-generated FASTQ files.
Dnaio
⭐
52
Efficiently read and write sequencing data from Python
Rattle
⭐
51
Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing
Dna Nn
⭐
51
Model and predict short DNA sequence features with neural networks
Metacache
⭐
49
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
Fastaq
⭐
45
Python3 scripts to manipulate FASTA and FASTQ files
Cfdnapattern
⭐
42
Pattern Recognition for Cell-free DNA
Bio
⭐
42
Bioinformatic infrastructure libraries
Assembly_improvement
⭐
39
Improve the quality of a denovo assembly by scaffolding and gap filling
Fuc
⭐
38
Frequently used commands in bioinformatics
Bioawk Tutorial
⭐
30
Bioinf Commons
⭐
30
Bioinformatics library in Kotlin
Faster
⭐
28
A (very) fast program for getting statistics about a fastq file, the way I need them, written in Rust
Orfipy
⭐
25
Fast and flexible ORF finder
Soap3 Dp
⭐
24
To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously.
Fusiondirect.jl
⭐
23
(No maintenance) Detect gene fusion directly from raw fastq files
Isonclust
⭐
23
De novo clustering of long transcript reads into genes
Iliad
⭐
21
ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications
Tiptoft
⭐
20
Predict plasmids from uncorrected long read data
Rna Seq Snakemake
⭐
20
Snakemake based pipeline for RNA-Seq analysis
Bioinfo
⭐
19
Various bioinformatics tools
Compression_benchmark
⭐
18
Benchmarking fastq compression with generic (mature) compression algorithms
Fasql
⭐
18
DuckDB Extension for reading and writing FASTA and FASTQ Files
Bio Tradis
⭐
15
A set of tools to analyse the output from TraDIS analyses
Micall
⭐
14
Pipeline for processing FASTQ data from an Illumina MiSeq to genotype human RNA viruses like HIV and hepatitis C
Snakemake Wrappers
⭐
14
🐍 Snakemake wrappers for bioinformatics.
Bipy
⭐
14
DEPRECATED Lightweight bioinformatics pipeline tools using iPython
Chia Pet_tool_v3
⭐
13
ChIA-PET, HiChIP, PLAC-Seq data analysis, with linker detection, linker filter, or restriction process for HiChIP, mapping, call cluster and visulization
Fast5seek
⭐
11
Subset of fast5 files contained in a fastq, BAM, or SAM file.
Destin
⭐
11
Toolkit for single-cell analysis of chromatin accessibility
Sequence Database Curator
⭐
10
This program dereplicates and/or filter nucleotide and/or protein database from a list of names or sequences (by exact match).
Pigx_bsseq
⭐
10
bisulfite sequencing pipeline from fastq to methylation reports
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.
Strandex
⭐
9
Sample an approximate number of reads from a fastq file without reading the entire file
Kf Alignment Workflow
⭐
9
🔬 Alignment workflow for Kids-First DRC
Fastqwiper
⭐
9
An ensamble method to recover corrupted FASTQ files, drop or fix pesky lines, remove unpaired reads, and fix reads interleaving.
Snakemake_rnaseq
⭐
8
A Snakemake pipeline to go from fastq mRNA sequencing files to raw and normalised counts (usable for downstream EDA and differential analysis)
Metacrast
⭐
8
MetaCRAST: reference-guided CRISPR detection in metagenomes
Hribo
⭐
8
We present HRIBO (High-throughput annotation by Ribo-seq), a workflow to enable reproducible and high-throughput analysis of bacterial Ribo-seq data. The workflow performs all required pre-processing steps and quality control. Importantly, HRIBO outputs annotation-independent ORF predictions based on two complementary prokaryotic-focused tools, and integrates them with additional computed features. This facilitates both the rapid discovery of ORFs and their prioritization for functional charact
Datools
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8
Java based bioinformatics data analysis tool kits
Fonda
⭐
7
Fonda is a framework which offers scalable and automatic analysis of multiple NGS sequencing data types
Rs_demultiplex
⭐
7
Simple demultiplexing of FASTQ, one oligo (barcode) at a time
Kutils
⭐
7
A random collection of kotlin utilities
Lava
⭐
6
LAVA: Longitudinal Analysis of Viral Alleles
Nohuman
⭐
6
Remove human reads from a sequencing run
Spritz
⭐
6
Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data
Metasequencing
⭐
5
A metagenomics pipeline using the CGAT framework.
Needletail
⭐
5
Fast k-mer methods in Rust
Bioinformatics One Liners
⭐
5
📝 Useful bioinformatics one-line commands.
Pistis
⭐
5
Quality control plotting for long reads
Fxtract
⭐
5
Extract sequences from a fastx file given a subsequence or identifier
Binf Scripts
⭐
5
A collection of useful bioinformatics scripts.
Fasta
⭐
5
This package enables you to deal with biological sequence files easily.
Ampliconnet
⭐
5
Sequence based 16S rRNA Taxonomic classifier using MLP
Mykrobe_tb_workflow
⭐
5
A workflow for analysis and resistance profiling of Mycobacterium tuberculosis nanopore data with Mykrobe
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