a-slide/BASH_NGS_Tools

This repository has been archived on 20/Jul/2023
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Created about 10 years ago
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a-slide/BASH_NGS_Tools

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Collection of simple NGS tools

pycoQC

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

NanoCount

EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2

pycoMeth

DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets

NanopolishComp

NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files

MetaCompore

Metacompore is a snakemake pipeline running multiple RNA modifications detection tools for nanopore directRNA sequencing

pycoSnake

pycoSnake is a neatly wrapped collection of snakemake workflows for analysing nanopore and Illumina sequencing data

Chimera_Finder

These BASH script allow to extract chimeric pairs and chimeric reads from NGS data mixing 2 DNA references

ContaVect

Complete suite to analyse DNA contaminants of virus/vector preparation from NGS data

Sekator

Multithreaded quality and adapter trimmer for PAIRED fastq files (Python2.7/Cython/C)

pyBioTools

Collection of tools to manipulate Bioinformatic standard file format + Generic file related function collection

blastpy3

Simple and lightweight Python 3 wrapper module for NCBI BLAST+

JupyterGenoViewer

JGV is a Python3 package for an embed genomic viewer in Jupyter notebook

Jupyter Notebook

Quade

Demultiplexer for PAIRED fastq files based on index sequence and PHRED quality (pure python)

MirStat

Simple tool to analyze miRNA QPCR data

fastq_control_sampler

Generates control fastq files R1 and R2 from fasta reference sequences

IsFinder

IsFinder find virus insertion site in host genomic DNA from pair end NGS data

pyFastq

Simple python 2.7 librarie to parse fastq files and handle illumina 1.8+ fastq sequences

pyBioPlot

High level library for Python 3 containing functions to generate specific plot for NGS and other biology related datasets.

Jupyter Notebook

Find_overlap_reads

Parse a BAM file and extract reads ovelapping given genomic coordinates

RScripts

Contains misc data specific R-cran scripts

py_NGS_tools

Collection of undocumented and experimental python tools related to NDS data

pyDNA

Collection of python 2.7 Utilities and Wrapper for DNA / NGS data manipulation

DNA_photolitography_seq

Repository containing analyses and datasets

Fast5Tools

Tools to manipulate Fast5 files

pyScripts

Contains misc data specific python3 scripts

Isis

ISIS generates random insertion sites of a given viral DNA in an host DNA and output Fastq Files

nanocompore_paper_analyses

Analyses performed for the nanocompore paper

Jupyter Notebook

versipy

Versatile version and medatada managment across the python packaging ecosystem with git integration

TargetPredict

Predict the targets of a short RNA in annotated features from genomic DNA, using BLAST, MIRANDA...