NGS-preprocess¶

NGS-preprocess is a pipeline developed with Nextflow and Docker. It was designed to provide an easy-to-use framework for preprocessing sequencing reads from Illumina, Pacbio and Oxford Nanopore platforms.

It wraps up the following tools:

Software	Analysis step	Source
sra-tools & entrez-direct	Interaction with SRA database for fetching fastqs and metadata	https://anaconda.org/bioconda/entrez-direct ; https://github.com/ncbi/sra-tools
Fastp	tool designed to provide fast all-in-one preprocessing for FastQ files	https://github.com/OpenGene/fastp
Porechop	ONT reads trimming and demultiplexing	https://github.com/rrwick/Porechop
pycoQC	ONT reads QC	https://github.com/tleonardi/pycoQC
NanoPack	Long reads QC and filter	https://github.com/wdecoster/nanopack
bax2bam	Convert PacBio bax files to bam	https://github.com/PacificBiosciences/bax2bam
bam2fastx	Extract reads from PacBio bam files	https://github.com/PacificBiosciences/bam2fastx
lima	PacBio reads demultiplexing	https://github.com/PacificBiosciences/barcoding
pacbio ccs	Generate PacBio Highly Accurate Single-Molecule Consensus Reads	https://ccs.how/

Support Contact¶

Feel free to contact me at almeidafmarques@gmail.com