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Minor typos #163

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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -364,7 +364,7 @@ Example:
polca.sh -a genome.fasta -r 'reads1.fastq reads2.fastq.gz' -t 16 -m 1G

## Chromosome scaffolder
The chromosome scaffolder tools allows to scaffold the assembled contigs using (large) reference scaffolds or chromosome sequences from the same or closely related species. For example, you've assembled a novel human genome and you wish to create a new reference genome with contigs placed on the chromosomes. The chromosome scaffolder will let you do exactly that. It will examine your contigs to see if there are any misassemblies in places where the contigs disagree with the reference using read alignments. The scaffolder will then break the contigs at all putative misassembled locations, creating clean contigs (you can disable that optionally). Then it will order and orient the clean contigs onto the chromosomes using the reference alignments. The scaffolder can be invoked as:
The chromosome scaffolder tools allows scaffolding the assembled contigs using (large) reference scaffolds or chromosome sequences from the same or closely related species. For example, you've assembled a novel human genome and you wish to create a new reference genome with contigs placed on the chromosomes. The chromosome scaffolder will let you do exactly that. It will examine your contigs to see if there are any misassemblies in places where the contigs disagree with the reference using read alignments. The scaffolder will then break the contigs at all putative misassembled locations, creating clean contigs (you can disable that optionally). Then it will order and orient the clean contigs onto the chromosomes using the reference alignments. The scaffolder can be invoked as:

chromosome_scaffolder.sh
-r <reference genome> MANDATORY
Expand All @@ -380,4 +380,4 @@ chromosome_scaffolder.sh
-M attempt to fill unaligned gaps with reference contigs: defalut off
-h|-u|--help this message

This tool is primarily designed for assemblies wigh good contiguity produced from long PacBio or Nanopore reads. The long reads (minimum 20x coverage) can be supplied with -s option. If you do not supply the lobg reads, you must set the -nb option which will skip splitting contigs and scaffold them as is. The -cl and -ch options set the coverage thresholds for splitting at suspect misassemblies, I recommend keeping -cl option at 3 and setting -ch option to about 1.5x the coverage of the long reads supplied with the -s option.
This tool is primarily designed for assemblies with good contiguity produced from long PacBio or Nanopore reads. The long reads (minimum 20x coverage) can be supplied with -s option. If you do not supply the long reads, you must set the -nb option which will skip splitting contigs and scaffold them as is. The -cl and -ch options set the coverage thresholds for splitting at suspect misassemblies, I recommend keeping -cl option at 3 and setting -ch option to about 1.5x the coverage of the long reads supplied with the -s option.