LAST |
Alignment |
adaptive seeds |
Adaptive seeds are matches that are chosen based on their rareness, instead of using fixed-length matches |
- |
the running time increases linearly with sequence length and short DNA reads |
https://gitlab.com/mcfrith/last |
21209072 |
Minimap2 |
Alignment |
split-read alignment |
DNA or long mRNA, higher accuracy, faster, and full length of reads |
- |
not suitable for chimeric alignments |
https://github.com/lh3/minimap2 |
29750242 |
GraphMap |
Alignment |
candidate alignments and fast graph traversal |
long reads with speed, high sensitivity |
- |
large-memory |
https://github.com/isovic/graphmap |
27079541 |
UNCALLED |
Alignment |
Ferragina-Manzini index |
mapping during sequencing and the leftmost mapping |
- |
not full length |
https://github.com/skovaka/UNCALLED |
33257863 |
tailfindr |
poly(A) |
measures poly(A) tail length |
- |
- |
- |
https://github.com/adnaniazi/tailfindr |
31266821, 33835460
|
NaS |
Assembly |
illumina hybrid |
entirely and with no error |
- |
Not suitable for large genomes |
https://www.genoscope.cns.fr/externe/nas/ |
25927464 |
LQS |
Assembly |
multiple-alignment corrected |
corrected by a multiple-alignment and 99.5% nucleotide identity |
- |
Not suitable for large genomes |
https://github.com/jts/nanopore-paper-analysis |
26076426 |
Canu |
Assembly |
tf-idf weighted MinHash and graph construction |
halves depth-of-coverage requirements, improves assembly continuity and reduces runtime on large genomes |
- |
accuracy depends on signal-level polishing |
https://github.com/marbl/canu |
28298431 |
Miniasm |
Assembly |
No correction |
magnitude faster |
- |
error rate is as high as raw reads |
https://github.com/lh3/miniasm |
27153593 |
Nanopolish |
Variant caller/Methylation detection |
Hidden Markov Model |
calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels |
- |
signal-level analysis |
https://github.com/jts/nanopolish |
26076426 |
Clairvoyante |
Variant caller/SV caller |
convolutional neural network |
SV calling, small variants and genotype |
- |
higher sequencing depth |
https://github.com/aquaskyline/Clairvoyante |
30824707 |
Clair |
Variant caller |
Deep neural network |
faster and complex variants with multiple alternative alleles |
- |
accuracy depends on pileup data and greater computational demands |
https://github.com/quay/clair |
|
NanoSV |
SV caller |
split- and gapped-aligned reads |
genotyping |
- |
non-detectable inversion, complex repeat regions and segmental duplications |
https://github.com/mroosmalen/nanosv |
29109544 |
Picky |
SV caller |
seed-and-extend process and split-read |
micro-insertions and phased SV |
- |
high specificity |
https://github.com/TheJacksonLaboratory/Picky |
29713081 |
NanoVar |
SV caller |
artificial neural network |
low-depth (8X) |
- |
the alignment profile of each read requires re-training |
https://github.com/benoukraflab/nanovar |
32127024 |
SENSV |
SV caller |
Deep neural network |
low-depth |
- |
balanced translocation missed |
https://github.com/HKU-BAL/SENSV |
|
CAMPHOR |
SV caller |
SV breakpoints |
polymorphic SVs and somatic SVs |
- |
removed indels in short repeats, the average read length 5 kbps and non-detectable indels < 100 bp |
https://github.com/afujimoto/CAMPHOR |
33910608 |
NanoMod |
Methylation detection |
signal intensities |
raw signal data and 5mC |
- |
two pair sample reads |
https://github.com/WGLab/NanoMod |
30712508 |
DeepSignal |
Methylation detection |
deep learning |
6mA/5mC, lower coverage, and predict methylation states |
- |
train DeepSignal to detect more types of base modification |
https://github.com/bioinfomaticsCSU/deepsignal |
30994904 |
mCaller |
Methylation detection |
neural network |
6mA and detect known or confirm suspected methyltransferase target motifs |
- |
only bacteria genome |
https://github.com/al-mcintyre/mCaller_analysis_scripts |
30718479 |
DeepMod |
Methylation detection |
recurrent neural network |
6mA/5mC,strand-sensitive and has single-base resolution |
- |
non-detectable other types of modifications or other different motifs, not suitable for RNA, neighboring bases inflence, elied on alignment tool to find correct reference positions of bases |
https://github.com/WGLab/DeepMod |
31164644 |
MINES |
Methylation detection |
random forest |
m6A sites within DRACH motifs |
- |
lost small difference modification sites and not suitable for DNA |
https://github.com/YeoLab/MINES |
31624092 |
Nanom6A |
Methylation detection |
XGBoost model |
m6A at single-base resolution and quantified abundance of m6A sites |
- |
not suitable for DNA |
https://github.com/gaoyubang/nanom6A |
33413586 |
FLAIR |
Isoform detection |
correct and realign |
assessing 3′ poly(A) tail length, base modifications, and transcript haplotypes |
- |
combined short Illumina reads |
https://github.com/BrooksLabUCSC/flair |
31740818 |
TrackCluster |
Isoform detection |
read tracks |
read classification, a transcript isoform with numerous exons, stage-specific or cell-specific expression of isoforms |
- |
not suitable for large genomes |
https://github.com/Runsheng/trackcluster |
32024662 |