Examples : samtools, bed, topic:conversion

13 tool(s) found

Tool Description Topics Available version(s)
AEGeAn CanonGFF3 pre-process GFF3 files, removing all features not directly related to protein-coding genes Genome annotation 1
AEGeAn GAEVAL compute coverage and integrity scores for gene models using transcript alignments. Genome annotation 1
AEGeAn LocusPocus calculate locus coordinates for the given gene annotation Genome annotation 1
AEGeAn ParsEval compare two sets of gene annotations for the same sequence. Genome annotation 1
breseq find mutations in haploid microbial genomes DNA mapping Genetic mapping Genome annotation Mapping assembly Protein SNP mapping Sequence word comparison 4
Find Nested Alternate ORFs (nAlt-ORFs) from BED and 2bit/FASTA Coding region prediction Codon usage analysis Codon usage table generation Genome annotation 1
Get Codon and Bicodon frequency from FASTA files Coding region prediction Codon usage analysis Codon usage table generation Genome annotation 1
Get Codon frequency from bicodons Coding region prediction Codon usage analysis Codon usage table generation Genome annotation 1
Integron Finder is a program that detects integrons in DNA sequences Genome annotation Nucleic acid sequence feature detection Protein sequence feature detection Sequence motif recognition 2
Map with BWA-MEM - map medium and long reads (> 100 bp) against reference genome DNA mapping Genetic mapping Genome annotation Mapping Mapping assembly Protein SNP mapping Sequence assembly Sequence tag mapping 14
Parallel Map with BWA for Illumina - map short reads (< 100 bp) against reference genome (mpi version) DNA mapping Genetic mapping Genome annotation Mapping Mapping assembly Protein SNP mapping Sequence assembly Sequence tag mapping 1
Prokka Prokaryotic genome annotation Coding region prediction Gene prediction Genome annotation 11
rose rank ordering of super-enhancers Genome annotation 1