Repeat Masking |
RepeatMasker |
4.1.1 |
Masks repeated sequences |
RepeatModeler |
2.0.1 |
de novo repeat masker |
Gene Prediction |
Augustus |
3.4.0 |
Eukaryotic gene predictor |
BRAKER2 |
2.1.5 |
Eukaryotic gene predictor |
GeneMarkES |
4.48 |
Eukaryotic gene predictor |
GeneMarkS |
4.32 |
Prokaryotic gene predictor |
Genscan |
1.0 |
Eukaryotic gene predictor |
Glimmer3 |
3.0.2 |
Prokaryotic gene predictor |
GlimmerM |
2.5.1 |
Eukaryotic gene predictor |
SNAP |
11/29/2013 |
Semi-HMM-based Nucleic Acid Parser, gene predictor |
Alignments |
BLAST+ |
2.12.0 |
Alignment tool for transcripts and proteins |
pBLAT |
2.5 |
Alignment tool for transcripts |
DIAMOND |
2.0.6 |
Alignment tool for protein evidence |
HISAT2 |
2.2.1 |
Aligns RNA-seq reads to genome |
PASA |
2.4.1 |
Aligns EST or transcript evidence |
TopHat |
2.1.1 |
Aligns RNA-seq reads to genome |
Genomic Features |
Getorf |
EMBOSS-6.6.0 |
Open reading frame finder |
RNAmmer |
1.2 |
Finds rRNA sequences |
SSR Finder |
N/A |
Finds user defined simple sequence repeats |
tRNAScan-SE |
2.0.7 |
Identifies tRNA sequences |
Consensus Gene Models |
EVidenceModeler |
1.1.1 |
Creates consensus gene structures for eukaryotes |
Functional Annotation |
BLAST+ |
2.12.0 |
Alignment tool for proteins |
DIAMOND |
2.0.6 |
Alignment tool for proteins |
InterProScan |
5.53-87.0 |
Classifies proteins by families and identifies functional domains |
Pfam |
1.6 |
Uses Pfam database to identify functional domains and families in proteins |
SignalP |
5.0 |
Predicts signal peptide cleavage sites in protein sequences |
TargetP |
2.0 |
Predicts the subcellular location of eukaryotic proteins based on signal peptide sequences |
Genome Browser |
Apollo |
2.0.7 |
Annotation editor |
JBrowse |
1.12.1 |
Genome browser |
Assembly/annotation metrics |
BUSCO |
5.2.2 |
Determines genome assembly and annotation completeness based on orthologs |
One code to find them all |
1.0 |
Reports repeat types from RepeatMasker |
PRINSEQ-lite |
0.20.4 |
Used to analyze assembly file for sequence number and size |