How to install and use proovread

This article introduces the relevant knowledge of "how to install and use proovread". In the operation of actual cases, many people will encounter such a dilemma, so let the editor lead you to learn how to deal with these situations. I hope you can read it carefully and be able to achieve something!

Proovread is a Pacbio sequence error correction software published on Bioinformatics in 2014. its basic principle is to correct the pacbio sequence by using the second generation short sequence with high accuracy and iterative alignment.

At present, the software has been made public on github and is constantly updated.

1. Installation of software

The installation method is relatively simple, just follow the official instructions.

two。 Usage

The use is also very simple, the input items that need to be set are relatively few, and most of them can be configured by default.

Proovread-t 8-l isoseq_flnc.fasta-s WT.trim_read1.fastq-s WT.trim_read2.fastq-p out_prefix

Parameter description:

-t: set the number of threads. The software consumes a lot of resources. If you want to speed up, you can set the number of threads larger.

-l: enter the sequence of pacbio

-s: is to input the short sequence of the second generation sequencing, if there are multiple files, you can enter it multiple times.

-p: specify the name of the output folder

3. Output result

* .trimmed.f [aq]: remove low quality and retain corrected high quality sequences * .untrimmed.fq: contains all sequences that are not corrected, low quality, and unfiltered

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