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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