Reapr
- reapr-break(1) make broken assembly via REAPR
- reapr-facheck(1) checks IDs in fasta file
- reapr-gapresize(1) calculates gap sizes based on read mapping
- reapr-perfectfrombam(1) generate perfect mapping plots from a bam file
- reapr-perfectmap(1) make perfect uniquely mapping plot files
- reapr-pipeline(1) run the REAPR pipeline
- reapr-plots(1) makes Artemis plot files for a given contig
- reapr-preprocess(1) preprocess files for REAPR run
- reapr-score(1) calculate scores and assembly errors
- reapr-seqrename(1) renames all sequences in a BAM file
- reapr-smaltmap(1) map read pairs using SMALT
- reapr-stats(1) generate REAPR stats from a BAM file
- reapr-summary(1) make REAPR summary stats file
- reapr(1) universal tool for genome assembly evaluation