wwood/kingfisher-download

Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

Language: Python - Size: 9.93 MB - Last synced at: 9 days ago - Pushed at: 24 days ago - Stars: 262 - Forks: 39

lskatz/fasten

:construction_worker: Fasten toolkit, for streaming operations on fastq files

Language: Rust - Size: 13.8 MB - Last synced at: 7 days ago - Pushed at: 11 days ago - Stars: 79 - Forks: 7

jordanlab/stringMLST

Fast k-mer based tool for multi locus sequence typing (MLST)

Language: Python - Size: 5.33 MB - Last synced at: 12 days ago - Pushed at: over 4 years ago - Stars: 44 - Forks: 7

stjude-rust-labs/fq

Command line utility for manipulating Illumina-generated FASTQ files.

Language: Rust - Size: 563 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 82 - Forks: 5

GiatrasKon/sandbox.bio-Solutions

Bash scripts replicating the commands from sandbox.bio's interactive bioinformatics tutorials, organized by categories such as Data Exploration, File Formats, Quality Control, and Data Analysis.

Language: Shell - Size: 11.7 KB - Last synced at: 21 days ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

Shogun486/Custom-DNA-mRNA-Sequence-Mapper

🧬 Automating the functionality of open-source program Minimap2

Language: Perl - Size: 5.86 KB - Last synced at: about 1 month ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

DKFZ-ODCF/FastqIndEx

A tool to index and extract data from gzipped FASTQ files

Language: C++ - Size: 3.75 MB - Last synced at: 3 months ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 1

iam28th/fqcomp28

Fast lossless entropy-based compressor for FASTQ files

Language: C++ - Size: 290 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

angelovangel/faster

A (very) fast program for getting statistics about a fastq file, the way I need them, written in Rust

Language: Rust - Size: 119 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 30 - Forks: 1

angelovangel/nanotimes

work with the time stamps of Oxford Nanopore (ONT) fastq files

Language: Rust - Size: 22.5 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0

FrietzeLabUVM/TAP

Pipeline to process RNAseq and ChIPseq data. Outputs include gene counts, transcripts per million, alternate splicing events, SNP calls, and bigwigs. Supports both Docker and Singularity for all dependencies.

Language: Shell - Size: 2.49 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0

stevekm/fastq-split

program for splitting a fastq file into separate files

Language: Go - Size: 51.8 KB - Last synced at: about 1 month ago - Pushed at: 11 months ago - Stars: 5 - Forks: 0

BioJulia/FASTX.jl

Parse and process FASTA and FASTQ formatted files of biological sequences.

Language: Julia - Size: 1.09 MB - Last synced at: 2 days ago - Pushed at: 6 months ago - Stars: 62 - Forks: 21

PopovIILab/BatShotMetaFlow

🦇🧫📊Supplementary materials for study on bat gut shotgun metagenomics

Language: HTML - Size: 29 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

angelovangel/fasterplot

A Rust program to calculate base yield over phred scores or base yield over length for a fastq file

Language: Rust - Size: 7.81 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

tbcgit/omdctk

OMD Curation Toolkit is a python package designed for the download and curation of metadata and fastq files of public omics datasets.

Language: Python - Size: 7.73 MB - Last synced at: 16 days ago - Pushed at: 12 months ago - Stars: 3 - Forks: 1

czbiohub-sf/crispycrunch 📦

Web app for CRISPR experiment setup and analysis

Language: Python - Size: 71.2 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 6 - Forks: 1

angelovangel/fastkmers

Obtain k-mer counts from fastx files

Language: Rust - Size: 72.3 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

nunofonseca/fastq_utils

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

Language: C - Size: 82 MB - Last synced at: 5 months ago - Pushed at: 9 months ago - Stars: 34 - Forks: 15

darlenewagner/NGS_Plot_Widgets

Provides graphical and .json output for paired-end Next-Generation Sequencing (NGS) data as well as genome coverage data from .bed files. Requires Python 3.9.1 or higher.

Language: Python - Size: 2.21 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

robiwangriff/ENA-submission-in-R

R functions and workflow for submitting amplicon sequence data to the ENA.

Language: R - Size: 246 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 1

rachadele/download-geo-fastqs

Download fastqs or supplementary files from GEO and upload to hca-util bucket

Language: Shell - Size: 77.1 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

lakhanp1/fastq_demultiplex

fastq demultuplexing util scripts

Language: Perl - Size: 4.84 MB - Last synced at: about 1 year ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 1

pughlab/ConsensusCruncher

ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to amalgamate reads derived from the same DNA template into a consensus sequence.

Language: Jupyter Notebook - Size: 51.6 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 21 - Forks: 10

BioJulia/ReadDatastores.jl

Datastores for reads, not your papa's FASTQ files.

Language: Julia - Size: 618 KB - Last synced at: 5 days ago - Pushed at: over 1 year ago - Stars: 11 - Forks: 4

refresh-bio/colord

A versatile compressor of third generation sequencing reads.

Language: C++ - Size: 5.53 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 45 - Forks: 10

DKFZ-ODCF/AlignmentAndQCWorkflows

The DKFZ alignment workflow plugin originally developed at the eilslabs

Language: Python - Size: 5.22 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 5

cartoonist/kseqpp

Fast FASTA/Q parser and writer (C++ re-implementation of kseq library)

Language: C++ - Size: 90.8 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 41 - Forks: 7

stevekm/squish

fastq file compression program

Language: Go - Size: 85 KB - Last synced at: about 1 month ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

mframpton/ArtificialFastqGenerator

Tool for generating artificial fastq files which can be used for testing the fidelity of NGS analysis pipelines.

Size: 1.38 MB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 4 - Forks: 3

jessievb/IDseq

R-package to analyse data from the immuno-detection by sequencing (ID-seq) technology.

Language: R - Size: 14.6 KB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 4 - Forks: 0

attayeb/auto-q

Auto-q Qiime Analysis Automating Script

Language: Python - Size: 75.2 KB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 3 - Forks: 1

angelovangel/nxf-bcl

A simple nextflow pipeline for Illumina run metrics (InterOp) and generation of fastq files (bcl2fastq)

Language: Nextflow - Size: 42 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 3

ALAPY/alapy_arc

ALAPY COMPRESSOR: FASTQ lossless compressor

Size: 4.94 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 9 - Forks: 1

GenomicaMicrob/pair-end_cleaner

Script to unzip, clean, assemble, and convert illumina pair-end fastq files in all subdirectories for 16S amplicon data (V3, V4 and V3-V4 regions).

Size: 8.79 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 2

raymondkiu/fastq-info

Calculate fastq reads and sequencing coverage

Language: Shell - Size: 58.6 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 12 - Forks: 2

evagunawan/SYLENS

SYLENS: Sampling Yielding LEss Noticeable Samples

Language: Python - Size: 641 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 1

yttria-aniseia/fastq-lengths

Language: C - Size: 20.5 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

Sarah-Hesham-2022/FASTQ_Files_Analysis

Data Analysis for Genomics, FASTQ File Structure and Analysis using Python.

Language: Python - Size: 547 KB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

judithbergada/Pipeline_GenomeAnalysis

Pipeline to assemble paired-end sequencing reads, annotate the resulting contigs, compare the genome content across sequences and determine the variants (SNPs).

Language: Shell - Size: 32.2 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

alastair-droop/fqtools

An efficient FASTQ manipulation suite

Language: C - Size: 2.28 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 127 - Forks: 16

ellisrichardj/BovTB-nf

Nextflow script for processing WGS data

Language: Shell - Size: 17.1 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 5

msk-access/merge_fastq

Package to merge multiple pair of pair-end fastq data

Language: Python - Size: 66.4 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 3 - Forks: 1

fhidalgor/mutagenesis_visualization

Software for the analysis and visualization of site-saturation mutagenesis experiments

Language: Python - Size: 67.8 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 13 - Forks: 2

shubhamchandak94/Spring

FASTQ compression

Language: C - Size: 45.2 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 79 - Forks: 17

Pinky-cloud224/snakemake_workflow_rna_seq_data_analysis

Language: Jupyter Notebook - Size: 975 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

openpaul/fqless

less like viewer for fastq files

Language: Shell - Size: 348 KB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 17 - Forks: 4

mattgalbraith/fastxtoolkit-docker-singularity

Build Docker container for FASTX Toolkit and (optionally) convert to Apptainer/Singularity.

Language: Dockerfile - Size: 1.95 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

adiamb/FASTQ_to_FASTA

A python script to convert FASTQ to FASTA

Language: Python - Size: 17.6 KB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 4 - Forks: 3

DKFZ-ODCF/nf-bam2fastq

Nextflow-based BAM-to-FASTQ conversion and FASTQ-sorting workflow.

Language: Shell - Size: 857 KB - Last synced at: 3 months ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 4

abhijeetsingh1704/fastA2Q

simple and convenient program to convert fasta sequences to fastq sequences

Language: Shell - Size: 42 KB - Last synced at: about 1 month ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 1

mnievesc/Ancient_mtDNA_Pipeline

Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.

Language: Shell - Size: 155 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 7 - Forks: 3

angelovangel/nxf-fastqc

A simple fastp-MultiQC nextflow pipeline

Language: Nextflow - Size: 36.5 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 5 - Forks: 3

michellejlin/lava

LAVA: Longitudinal Analysis of Viral Alleles

Language: Python - Size: 53.5 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 8 - Forks: 7

schosio/GUFETCH

A GUI tool to download SRA files

Language: Shell - Size: 38.1 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

angelovangel/nextflow-fastp-shiny

a shiny frontend for the nextflow-fastp pipeline

Language: R - Size: 9.72 MB - Last synced at: about 2 years ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 1

alex-merge/PyFastaTools

Tools to analyze fasta or fastaq files with python.

Language: Python - Size: 203 KB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

biodata-fun/htslib_howto

Collection of simple C scripts for parsing vcf or bam files using the htslib C library. These scripts can be used as the starting point for more complex scripts

Language: C - Size: 16.6 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 11 - Forks: 1

pentalpha/luthien

Super ultra-fast fastq preprocessor, using parallel windowed adaptive trimming.

Language: C++ - Size: 354 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

angelovangel/fastjac

k-mer similarity metrics for two fastx files

Language: Rust - Size: 5.86 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

AmirHoseinSafari/Genotype-collector-and-SNP-dataset-creator

Collecting Genotypes from ENA and make their SNPs

Language: Python - Size: 40 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 5 - Forks: 0

gdefazio/SplitFastq

It splits a fastq file containing R1 and R2 reads.

Language: C - Size: 1.95 KB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

aaiezza/FLiCK

FLiCK - Format LeveragIng Compression frameworK

Language: Java - Size: 1.36 MB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 2 - Forks: 0

pentalpha/sickle Fork of najoshi/sickle

Parallel Windowed Adaptive Trimming for fastq files using quality

Language: C++ - Size: 559 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

mandyjker/filter_fastq_files

3 programs in C that filter .fastq files

Language: C - Size: 22.5 KB - Last synced at: 26 days ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

AmyL19/DriverFinder

Size: 21.7 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

eachanjohnson/gordium

Fast demultiplexing of Illumina FASTQ files using Python.

Language: Python - Size: 6.84 KB - Last synced at: about 2 years ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 0