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bash_utilities

contavect

Analyse DNA contaminants from NGS data

designer

sh-miR Designer is a software aimed for fast and efficient design of effective RNA interference (RNAi) reagents - sh-miRs, also known as artificial miRNAs.

fastq_control_sampler

Generates control fastq files R1 and R2 from fasta reference sequences

my_ipython_notebook

All ipython notebook

ncbi_search

Quick Tools

ntcontent

pbrandomreads

py

pyblast

Simple and lightweight Python 2/3 wrapper module for NCBI BLAST+

pydna

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

pyfastq

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

quade

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

refmasker

Hard mask homologies between fasta reference sequences identified by Blastn

sam2sql

samfields

Creation of histogram(s) representing the number of reads depending of MAPQ, AS, or NM SAM field.

sekator

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

ssv-conta

SSV-Conta quantify and characterize DNA contaminants from gene therapy vector sequenced by Illumina system.

ssv-coverage

Coverage graph creator from BAM files (included in the SSV-Conta package)

utilities

vardict

VarDict

vardictjava

VarDict Java port