gravatar for chen

2 hours ago by

OpenGene

Hi, I am the author of fastp and many other open source tools.

Today, I want to introduce my new work, fastv, an ultra-fast tool for detecting viral sequence from sequencing data for detection of viral infectious diseases, like COVID-19.

This tool accepts the input of raw or clean FASTQ files (both SE/PE), performs quality filtering as fastp does (cut adapters, remove low quality reads, correct wrong bases), and then scans the clean data for the viral sequences.

fastv is an OpenGene project: github.com/OpenGene/fastv

take a quick glance of the informative report

try fastv to generate above reports

quick examples

Single-end data

./fastv -i testdata.fq.gz

Paired-end data

./fastv -i R1.fq.gz -I R2.fq.gz

screenshot

image

For more information, go: github.com/OpenGene/fastv

link

modified 2 hours ago

written
2 hours ago
by

chen1.9k



Source link