Table 1 Tools developed for processing next-generation sequencing data

FastQC

Quality check

Java

PIQA

Quality check

R,C++

FASTX-Toolkit

A collection of tools to filter low quality reads and remove adapters

C,C++

Fqtools

FASTQ file manipulation, such as validate FASTQ and trim reads in a FASTQ file

C

seqtk

Toolkit for processing sequences in FASTA/Q formats, such as format conversion and subsampling of sequences

C

PRINSEQ

Filter, reformat and trim sequences

Perl, R

Multiqc

Aggregate results across many samples into a single report

Python

NGS QC Toolkit

Filter low quality reads and remove adapters.

Perl

Fastp

Filter low quality reads and trim adapters

C++

FaQCs

Filter low quality reads and trim adapters

C++