• Kraken: Kraken is the first taxonomic classification software released by these authors. When released, Kraken introduced exact k-mer matching and a novel classification algorithm to achieve high sensitivity and speed as compared to previous classification programs.
  Kraken是最早开发的一个版本，利用的是k-mer比对算法。

• KrakenUniq: KrakenUniq, released in 2018, is based on Kraken 1, using the same databases and classification algorithm. However, while Kraken provides only the read counts, KrakenUniq also determines the k-mer coverage for each taxonomic classification. This metric can assist in filtering false positive reads.
  KrakenUniq is only compatible with Kraken 1, not Kraken 2
  KrakenUniq 基于Kraken 1 ，特点是除了提供read计数外，还提供每个物种的k-mer覆盖度。不兼容Kraken2

• Kraken 2: Kraken 2, released in 2018, has significant memory and speed improvements while maintaining the original Kraken classification algorithm and k-mer based classification.
  Kraken2做了内存和速度优化。

• Centrifuge: Centrifuge, released in 2016, is the first software written to address the memory issues of Kraken. Written as an entirely new software by Daewhan Kim, Li Song, and Florian P Breitwieser, Centrifuge creates significantly smaller databases based on an FM-index and compression of within-species genomes. However, Centrifuge also uses an entirely different classification algorithm (described in further detail below)
  Centrifuge做了内存优化以及使用了完全不同的分类算法。

• Bracken: Bracken is compatible with Kraken 1, Kraken 2, and KrakenUniq as a post- processing script.
  All software in the Kraken world are taxonomic classification programs. While these programs attempt to assign each read a specific label, some reads may match kmers shared between two distantly related taxon, causing the read to be labeled at a "higher" taxonomic level (such as Bacteria).
  For a more comprehensive picture of a sample's composition, Bracken is provided as a post-processing software, estimating abundance estimation at any desired taxonomic level (e.g. species or genus abundance estimation). This therefore allows users to see the estimated composition of their sample at a particular taxonomic level.
  There is a plan to integrate KrakenUniq's coverage information to help inform the abundance estimation performed by Bracken
  Bracken是一个后处理脚本，对每个物种级别进行丰度估计。

• Pavian: All of the above software provide output files in text format per sample. Pavian was developed in 2016 to allow Kraken and Centrifuge users both visualize the classification results AND compare between samples.
  可视化工具

Kraken1已经淘汰，不建议使用。
KrakenUniq更适合严格的病原检测场景，对假阳性比较敏感的情况。但是Kraken2资源需求较低，支持的数据库比较多。

Centrifuge资源需求最低，但是一条read会给出多个匹配，Kraken2只会给出一个匹配。Kraken2速度更快。而且Bracken不支持Centrifuge。

对于病原鉴定的场景，我们建议使用KrakenUniq+Bracken的方式。
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1568-0
上面KrakenUniq的这篇文献也提到了比对和组装的问题，文章认为比对比较慢，组装可能不太现实，因为阳性的物种序列数可能本身就比较少。