./GATK_polish.sh 
Usage: GATK_polish.sh <Assembly to polish (.fa)> <Reads 1> <Reads 2> <# threads>

./racon_polish.sh 
Usage: racon_polish.sh <Assembly to polish (.fa)> <Reads 1> <Reads 2> <# threads>

./pilon_polish.sh 
Usage: pilon_polish.sh <Assembly to polish (.fa)> <Reads 1> <Reads 2> <# threads>

====
This is the ntEdit PAPER version

1) NTHITS

nthits --help
Usage: nthits [OPTION]... FILES...
Reports the most frequent k-mers in FILES(>=1).
Accepatble file formats: fastq, fasta, gz, bz, zip.

 Options:

  -t, --threads=N	use N parallel threads [16]
  -k, --kmer=N	the length of kmer [64]
  -c, --cutoff=N	the maximum coverage of kmer in output
  -p, --pref=STRING	the prefix for output file name [repeat]
  --outbloom	output the most frequent k-mers in a Bloom filter
  --solid	output the solid k-mers (non-errornous k-mers)
  --help	display this help and exit
  --version	output version information and exit

Report bugs to hmohamadi@bcgsc.ca.




NOTE: In the latest release of nthits, you must run it like this:

nthits -c 1 -k 50 -t 48 -p solidBF --outbloom @reads.in

where @reads.in lists all reads to kmerize

note the options --outbloom and -p that must be set 

If not specifying a hard threshold (-c), and relying instead on ntCard* to identify the error kmer coverage, please run with the --solid:

nthits -k 50 -t 48 --outbloom --solid @reads.in 

NOTE: THIS WILL WORK WELL WITH ntEdit ONLY IF YOU HAVE SUFFICIENT READ COVERAGE (>40X), OTHERWISE SET KMER COVERAGE TO -c1


*Bioinformatics. 2017 May 1; 33(9): 1324–1330.
Published online 2017 Jan 5. doi: 10.1093/bioinformatics/btw832
PMCID: PMC5408799
PMID: 28453674
ntCard: a streaming algorithm for cardinality estimation in genomics data
Hamid Mohamadi,1,2 Hamza Khan,1,2 and Inanc Birol1,2


2) NTEDIT

ntedit --help
Usage: ntEdit 
genome assembly polisher 


 Options:
	-t,	number of threads [default=1]
	-f,	Draft genome assembly (FASTA, Multi-FASTA, and/or gzipped compatible), REQUIRED
	-r,	Bloom filter file (generated from ntHits), REQUIRED
	-b,	output file prefix, OPTIONAL
	-k,	kmer size, REQUIRED
	-z,	minimum contig length [default=100]
	-i,	maximum number of insertion bases to try, range 0-5, [default=4]
	-d,	maximum number of deletions bases to try, range 0-5, [default=5]
	-x,	k/x ratio for the number of kmers that should be missing, [default=5.000]
	-y, 	k/y ratio for the number of editted kmers that should be present, [default=9.000]
	-v,	verbose mode (-v 1 = yes, default = 0, no)

	--help,		display this message and exit 
	--version,	output version information and exit
Report bugs to rwarren@bcgsc.ca

./ntEdit.pl -f pacbio.fasta -k 50 -r solidBF_k50.bf -x 5 -y 9 -b pac_nteditk50i0d0x5y9z