AkiShiroma

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rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

Language:RNOASSERTION1316 183 41

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Language:NextflowMIT825 152 631

deepTools

Tools to process and analyze deep sequencing data.

Language:PythonNOASSERTION666 37 930

biotools

A list of useful bioinformatics resources

hpc-container-maker

HPC Container Maker

Language:PythonApache-2.0444 24 64

composer

Visual and code editor for Common Workflow Language

Language:TypeScriptApache-2.0301 23 97

Filtlong

quality filtering tool for long reads

Language:C++GPL-3.0274 14 37

shasta

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

Language:C++NOASSERTION270 23 106

ngsplot

Quick mining and visualization of NGS data by integrating genomic databases

Language:RNOASSERTION251 25 93

pycoQC

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)

Language:PythonGPL-3.0250 5 98

Long-read-assembler-comparison

Benchmarking of long-read assembly tools for bacterial whole genomes

Language:PythonCC-BY-4.0169 15 4

LongQC

LongQC is a tool for the data quality control of the PacBio and ONT long reads.

Language:CMIT139 1 74

TALON

Technology agnostic long read analysis pipeline for transcriptomes

Language:PythonMIT133 5 140

NECAT

Nanopore data assembler

Language:C132 9 55

any2fasta

Convert various sequence formats to FASTA

Language:PerlGPL-3.0126 5 24

LongRead_tutorials

Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data

GPL-3.0120 6 9

taiyaki

Training models for basecalling Oxford Nanopore reads

Language:PythonNOASSERTION113 40 101

pipeline-transcriptome-de

Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads

Language:PythonNOASSERTION106 21 31

Peregrine

Peregrine: Fast Genome Assembler Using SHIMMER Index

Language:Jupyter NotebookNOASSERTION99 8 35

master_of_pores

Nextflow pipeline for analysis of direct RNA Nanopore reads

Language:NextflowMIT88 9 111

AGB

Interactive visualization of assembly graphs

Language:JavaScriptNOASSERTION78 6 12

qcat

qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.

Language:PythonMPL-2.077 190

conterminator

Detection of incorrectly labeled sequences across kingdoms

Language:CGPL-3.075 5 23

helen

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

Language:PythonMIT68 6 27

tiny-test-data

Super small biological datasets for unit testing

Language:PythonMIT61 8 3

FindTelomeres

A python script for finding telomeric repeats (TTAGGG/CCCTAA) in FASTA files

Language:PythonGPL-3.031 2 1

SGTK

Example of SGTK application for E.coli dataset:

Language:JavaScriptNOASSERTION29 6 7

nanoflow

:microscope: De novo assembly of nanopore reads using nextflow

Language:NextflowGPL-3.020 8 8

NGS_HandsOnWorkshop

Hands-on workshop on NGS data analysis @ NARO

Language:Shell11 10

rnaseq_workshop

Cleveland Clinic Bioinformatics Workshop for RNA-Seq data analysis

6 30