| 1 |
Fulgor |
Taxonomic classification |
https://link.springer.com/article/10.1186/s13015-024-00251-9 |
https://github.com/jermp/fulgor |
Table 2 (only for E.coli) |
|
| 2 |
Sourmash |
Phylogenetic similarity |
https://f1000research.com/articles/8-1006/v1 |
https://github.com/sourmash-bio/sourmash |
Figure 3 |
|
| 3 |
Kraken2
|
Taxonomic classification |
https://link.springer.com/article/10.1186/s13059-019-1891-0/figures/2 |
Software:
https://ccb.jhu.edu/software/kraken/
Databases:
https://benlangmead.github.io/aws-indexes/k2
|
Figure 2 (a,b and c only for Kraken2) |
|
| 4 |
CLARK |
Taxonomic classification |
https://link.springer.com/article/10.1186/s12864-015-1419-2
|
http://clark.cs.ucr.edu/ |
Table 1 and 2 only for Clark-l and HiSeq data |
|
| 5 |
Metakallisto |
Taxonomic classification |
https://www.nature.com/articles/nbt.3519
https://arxiv.org/abs/1510.07371
|
https://github.com/pachterlab/metakallisto?tab=readme-ov-file |
Table 2 |
|
| 6 |
MetaGraph |
Taxonomic classification |
https://www.biorxiv.org/content/10.1101/2020.10.01.322164v4 |
https://github.com/ratschlab/metagraph
https://metagraph.ethz.ch/
|
Figure 1 a and b only for Metagraph |
|
| 7 |
Centrifuge |
Taxonomic classification |
https://genome.cshlp.org/content/26/12/1721.short |
http://ccb.jhu.edu/software/centrifuge/ |
Figure 3 |
|
| 8 |
Blast+ |
Taxonomic classification |
https://link.springer.com/article/10.1186/1471-2105-10-421 |
https://blast.ncbi.nlm.nih.gov/ |
Figure 3 |
|
| 9 |
Pufferfish |
Taxonomic classification |
https://academic.oup.com/bioinformatics/article/34/13/i169/5045749 |
https://github.com/COMBINE-lab/pufferfish |
Table 2 only for human and pufferfish |
|
| 10 |
Themisto |
Taxonomic classification |
https://academic.oup.com/bioinformatics/article/39/Supplement_1/i260/7210444 |
https://github.com/algbio/themisto |
Figure 6 contruction time and construction peak memory for themisto (up to 1000 genomes) |
|
| 11 |
Stat |
Host contamination removal |
Host contamination removal with STAT
https://doi.org/10.1186/s13059-021-02490-0
|
https://github.com/ncbi/sra-human-scrubber |
Table 1 |
|
| 12 |
Hostile |
Host contamination removal |
https://doi.org/10.1093/bioinformatics/btad728 |
https://github.com/bede/hostile |
Table 1 (only Hostile, without Mycobacteria) |
|
| 13 |
Metaspades |
Assembly |
https://genome.cshlp.org/content/27/5/824.short |
https://github.com/ablab/spades |
Table 1 HMP only for Metaspades |
|
|
| 14 |
hifiasm-meta |
Assembly |
https://www.nature.com/articles/s41592-022-01478-3 |
https://github.com/xfengnefx/hifiasm-meta |
Table 1, Human V1 (downsampled to fit in RAM) |
|
| 15 |
MegaHit |
Assembly |
https://academic.oup.com/bioinformatics/article/31/10/1674/177884 |
https://github.com/voutcn/megahit |
Table 1 without Spades |
|
| 16 |
metaMDBG
|
Assembly |
https://www.nature.com/articles/s41587-023-01983-6 |
https://github.com/GaetanBenoitDev/metaMDBG |
Figure 2 a) only for metaMDBG |
|
|
| 17 |
Rhea |
Structural variant detection |
https://academic.oup.com/bioinformatics/article/40/Supplement_1/i58/7700881#468774272 |
https://github.com/treangenlab/rhea |
Table 1 |
|
| 18 |
Dada2 |
Error correction for Illumina reads |
https://doi.org/10.1038/nmeth.3869 |
https://github.com/treangenlab/rhea |
Figure 1 a) |
|
| 19 |
metagenomeSeq |
Differential abundance analysis |
https://www.nature.com/articles/nmeth.2658#Sec12 |
R Bioconductor package |
Figure 2 b) |
|
| 20 |
Ebay |
Differential abundance analysis |
https://link.springer.com/article/10.1186/s12859-020-03552-z |
https://github.com/liudoubletian/eBay |
Figure 1 only for ebay and metagenomeseq (t-test and wilcoxon test) |
|
| 21 |
Omnibus |
Differential abundance analysis |
https://academic.oup.com/bioinformatics/article/34/4/643/4470360?login=true |
https://github.com/jchen1981/MicrobiomeDDA |
Figure 8 (COMBO dataset) |
|
