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493 search results found

QTL-seq pipeline to identify causative mutations responsible for a phenotype

Assembly_improvement ⭐ 39

Improve the quality of a denovo assembly by scaffolding and gap filling

Transcriptomeassemblytools ⭐ 39

A collection of scripts for processing fastq files in ways to improve de novo transcriptome assemblies, and for evaluating those assemblies.

Frequently used commands in bioinformatics

Fasta_utilities ⭐ 37

A collection of scripts developed to interact with fasta, fastq and sam/bam files.

Plate_scatac Seq ⭐ 37

A rapid and robust plate-based single cell ATAC-seq (scATAC-seq) method

In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution), a p-value for each call, and the expression of each class.

Antonie is an integrated, robust, reliable and fast processor of DNA reads

VDJ assignment and antibody sequence annotation. Scalable from a single sequence to billions of sequences.

Analysis Framework for Biological Data from High Throughput Experiments

Calib clusters barcode tagged paired-end reads based on their barcode and sequence similarity.

Deep learning library for biological sequences. Extension of Fastai and Pytorch.

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

Utility program for extracting sequences from a fasta/fastq file

Paired Tag ⭐ 33

Analysis of Paired-Tag datasets

Blast2bam ⭐ 33

Blast2Bam uses the XML results of Blastn, the reference and the fastQ or fasta file(s) to output a SAM file.

Full-length transcriptome splicing and mutation analysis

Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences

Athena_meta ⭐ 31

read cloud assembler

Ngs_pipeline ⭐ 31

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Naive de Bruijn graph implementation in python

Fastqc Rs ⭐ 31

A quality control tool for FASTQ files written in rust

Bioinf Commons ⭐ 30

Bioinformatics library in Kotlin

Bioawk Tutorial ⭐ 30

Sff2fastq ⭐ 30

extract 454 Genome Sequencer reads from a SFF file and convert them into a FASTQ formatted output

Rna Seq_notes ⭐ 29

A continually expanding collection of RNA-seq tools

Fastq Rs ⭐ 29

Fastq_utils ⭐ 29

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

Bcbiosinglecell ⭐ 29

R package for bcbio single-cell RNA-seq analysis.

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

Bam2fastx ⭐ 28

Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files.

Gem3 Mapper ⭐ 27

Readability enhancement tool for bioinformatics data file format

deBGR: An Efficient and Near-Exact Representation of the Weighted de Bruijn Graph

QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.

Mpraflow ⭐ 27

A portable, flexible, parallelized tool for complete processing of massively parallel reporter assay data

Smart Seq3 ⭐ 27

Code and analysis pipeline for Smart-seq3 (Hagemann-Jensen et al. 2020).

A python program to call methylation (m6A in DNA) from nanopore signal data

Demultiplex ⭐ 26

Versatile FASTA/FASTQ demultiplexer.

Fastascripts ⭐ 26

Manipulate FASTA files

An approximate sequence pattern matcher for FASTQ/FASTA files.

FxTools: a comprehensive toolkit for FASTA and FASTQ file manipulation

Fast and flexible ORF finder

Split Seq_demultiplexing ⭐ 25

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

Ublastx_stageone ⭐ 24

This is the source code for multisamples ARGs profiling using SARG2.0 database

An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters

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.

Fastq Scan ⭐ 24

Output FASTQ summary statistics in JSON format

Analyze NGS data for CRISPR (or any engineered endonuclease) activity and screen for clones. Screen for NHEJ or multiple HDR events concurrently.

Brb Seqtools ⭐ 24

Suite of tools for processing BRB-seq data

This repository is deprecated, please use the link to the right.

Isonclust ⭐ 23

De novo clustering of long transcript reads into genes

Fusiondirect.jl ⭐ 23

(No maintenance) Detect gene fusion directly from raw fastq files

Readshift ⭐ 23

Readshift: A method to shift high-quality NGS datasets into noisy datasets

Known and Novel IsoForm Explorer. Statistically based splicing detection for circular and linear isoforms

fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads

mapping pipeline for ancient DNA

Germline Dna ⭐ 23

A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample

Site Identification from Short Read Sequences.

Fastdemultiplexer ⭐ 22

A sequence demultiplexer for the Illumina HiSeq technology

Pfastq Dump ⭐ 22

parallel-fastq-dump implementation in bash script

A unified array job submitter for LSF, SGE/UGE and Slurm

SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA

Allbiotc2 ⭐ 22

Benchmark pipeline for Structural Variation analyses, funded by the ALLBio.

Chip Seq_preprocess ⭐ 21

A preprocessing pipeline for ChIP-seq, including alignment, quality control, and visualization.

Biohansel ⭐ 21

Rapidly subtype microbial genomes using single-nucleotide variant (SNV) subtyping schemes

ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications

RNAseq pipeline centered on Salmon

Linked-Read Alignment Tool

Fastq Multx ⭐ 21

Demultiplexes a fastq.

Amplicon_sorter ⭐ 21

Sorts amplicons from Nanopore sequencing data based on similarity

Open-source bioinformatics pipeline for the preprocessing of raw sequencing data.

Automated human exome/genome variants detection from FASTQ files

Rna_velocity_quant ⭐ 21

Evaluation of the effect of quantification choices on RNA velocity estimates

Gsufsort ⭐ 21

gsufsort: building suffix arrays, LCP-arrays and BWTs for string collections [AMB 2020]

Nanolyse ⭐ 21

Remove lambda phage reads from a fastq file

Pipeline Umi Amplicon ⭐ 21

Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers

Rnaseq Nf ⭐ 20

RNAseq analysis pipeline

Predict plasmids from uncorrected long read data

Ultra-fast Multi-threaded FASTQ Demultiplexing

Rna Seq Snakemake ⭐ 20

Snakemake based pipeline for RNA-Seq analysis

Pipelines ⭐ 20

Aligner for sequencing data

Highperformancengs ⭐ 20

hight performance & useful tools for working with fastq and bam files

Utilities for large scale distributed single cell data processing

Fastrationals.jl ⭐ 20

Arithmetic with small and with very large rationals is made fast.

Assembler Components ⭐ 20

Components of genome sequence assembly tools

An ultra fast and accurate paired-end adapter trimmer that needs no a priori adapter sequences.

Pipeline Nanopore Denovo Isoforms ⭐ 19

Pipeline for de novo clustering of long transcriptomic reads

CWL tools and workflows for GGR

Various bioinformatics tools

Java Bindings (JNI) for bwa

Seqqscorer ⭐ 18

A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample

An error model and pipeline for analyzing deep mutational scanning (DMS) data and diagnosing common experimental pathologies

Sc Rna Seq Pipeline ⭐ 18

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