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Search results for genome fastq

75 search results found

Bactopia ⭐ 281

A flexible pipeline for complete analysis of bacterial genomes

Pyfastx ⭐ 211

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

Randomly subsample sequencing reads to a specified coverage

Viral Ngs ⭐ 129

Viral genomics analysis pipelines

Pipeline Structural Variation ⭐ 87

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

Genefuse ⭐ 86

Gene fusion detection and visualization

Mcclintock ⭐ 83

Meta-pipeline to identify transposable element insertions using next generation sequencing data

Nullarbor ⭐ 80

💾 📃 "Reads to report" for public health and clinical microbiology

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.

Metacache ⭐ 49

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

W2rap Contigger ⭐ 44

An Illumina PE genome contig assembler, can handle large (17Gbp) complex (hexaploid) genomes.

Pauvre: QC and genome browser plotting Oxford Nanopore and PacBio long reads.

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

Bioinf Commons ⭐ 30

Bioinformatics library in Kotlin

Sff2fastq ⭐ 30

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

Gem3 Mapper ⭐ 27

An approximate sequence pattern matcher for FASTQ/FASTA files.

Fastq Scan ⭐ 24

Output FASTQ summary statistics in JSON format

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

Site Identification from Short Read Sequences.

Nanolyse ⭐ 21

Remove lambda phage reads from a fastq file

Automated human exome/genome variants detection from FASTQ files

Pipeline Umi Amplicon ⭐ 21

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

Biohansel ⭐ 21

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

Rnaseq Nf ⭐ 20

RNAseq analysis pipeline

Assembler Components ⭐ 20

Components of genome sequence assembly tools

Aligner for sequencing data

Aligner for sequencing data

Seqqscorer ⭐ 18

4C-seq processing pipeline

Tracespipe ⭐ 16

Reconstruction and analysis of viral and host genomes at multi-organ level

Rna Seq Qc ⭐ 16

Rna-seq pipeline, From FASTQ to differential expression analysis...

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

Rnaquast ⭐ 13

Quality assessment of de novo transcriptome assemblies from RNA-Seq data

Microbiome Classifier Pipeline for Pacific Biosciences 16s Data

Sequencing_for_genetics ⭐ 11

유전학자를 위한 시퀀싱 자료 분석

Kmerspectrumanalyzer ⭐ 11

Clipseqtools ⭐ 11

A suite for the analysis of CLIP-Seq datasets.

Nuc_processing ⭐ 11

Chromatin contact paired-read single-cell Hi-C processing module for Nuc3D and NucTools

Relocate2 ⭐ 10

Pigx_bsseq ⭐ 10

bisulfite sequencing pipeline from fastq to methylation reports

Red-C data processing

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)

Bioscripts ⭐ 10

a bucket of bioinformatics scripts

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

Hichap_master ⭐ 9

An integrated package to process diploid Hi-C data

Hierarchical Genome Assembly Hga ⭐ 9

Hierarchical genome assembly: de novo bacterial genome assembly using high coverage short sequencing reads

Sparseassembler ⭐ 8

A sparse k-mer graph based, memory-efficient genome assembler.

Targeted Amplicon Bisulfite Sequencing Analysis Tool

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

Copy number estimation of highly duplicated sequences

Staphopia Ap ⭐ 7

Digestion template-based deconvolution for chromatin structure inference.

Mag_snakemake_wf ⭐ 7

Recovery of prokaryotic genomes from shotgun metagenomic sequencing data

Pipelines for assembling NGS data from Seattle flu study.

Estimating and predicting HiC library resolution

St_pipeline ⭐ 6

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.

Fastqsifter ⭐ 6

Separate contaminating reads from FASTQ files (e.g., mitochondria, symbionts, bacterial or human contaminants)

Genome Analysis Tutorial ⭐ 6

The Genome Analysis Tutorial Page.

Pipeline for CnR, CnT

egaz and alignDB work with external (NCBI/EBI) data

Nascent Transcription Processing Pipeline

Fastq Info ⭐ 6

Calculate fastq reads and sequencing coverage

Measurement of Allelic Ratio Informatics Operator (MARIO) pipeline

Targeted and Mapping-Free Variant Calling in FastQ Reads of Bacterial Genomes

Kodoja: identifying viruses from plant RNA sequencing data

Reference-free FASTQ filter for rare germline and somatic variants

Guttman_ismagilov_labs ⭐ 5

Mugqic_pipelines ⭐ 5

Open Science Grid Workflow That Creates Gene Expression Matrices (GEMs) from SRA/FASTQ NGS Files

Poolparty ⭐ 5

Whole-genome bioinformatic pipeline for pooled or individual-based NGS data using bash and R

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