2019-04-13 LoRMA 使用笔记

想做三代测序数据校正时候发现的。

开始是在看LoRDEC，想知道能否LoRDEC做self correction，说明中发现这一条,就尝试一下。

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2.8 Can LoRDEC perform also self-correction?

Not directly. However, LoRDEC has a companion software called LoRMA, that uses LoRDEC and performs self-correction with long reads. LoRMA does not need short reads, but use only long reads. For the same amount of data, LoRMA requires more computing resources and more time. LoRMA can be downloaded from http://www.cs.helsinki.fi/u/lmsalmel/LoRMA/.

Reference: Accurate self correction of errors in long reads using de Bruijn graphs

L. Salmela, R. Walve, E. Rivals, E. Ukkonen. Bioinformatics, 33 (6): 799-806, 10.1093/bioinformatics/btw321, 2017.

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安装

官网 https://gite.lirmm.fr/lorma/lorma-releases/wikis/home

    conda install -c atgc-montpellier lorma

conda install -c atgc-montpellier lordec

两个是姊妹软件，lorma需要借助lordec才能用，需要一起安装。

#### 介绍

LoRMA proceeds in two phases.

It iteratively performs local correction of the long reads using LoRDEC (with one special option). The number of LoRDEC iterations is set by the user.

It then corrects the long read using long-range sequence similarity, which it detects by clustering similar reads using a heuristic multiple alignment procedure.

在/home/Acer1/anaconda2/bin中，命令行直接调用lorma.sh就可以使用了