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link to new, recommended DOI resolver in README.md #49

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Expand Up @@ -107,7 +107,7 @@ Aligning is a computationally intensive process and will take far more CPU time

Many of the Hi-C reads can be determined to be noise, rather than signal. It is not strictly necessary to remove these reads from your BAM files before running LACHESIS. But it will reduce the files' size, reduce the I/O time required by LACHESIS to read them in, and may reduce LACHESIS' error rate.

We have included the scripts `PreprocessSAMs.pl` and `PreprocessSAMs.sh`, which perform the filtering methods we used. `PreprocessSAMs.pl` removes all reads that do not map within 500bp of a restriction enzyme site, following the suggestion of [Yaffe & Tanay (Nature Genetics, 2011)](dx.doi.org/10.1038/ng.947). To do this, it uses the script `make_BED_around_RE_site.pl` (also included) and also the bedtools library. `PreprocessSAMs.pl` also removes unpaired reads, which LACHESIS cannot use. Make sure to set the variable `$RE_site` in `PreprocessSAMs.pl`. You can also use the script `PreprocessSAMs.sh` as a batch script to run `PreprocessSAMs.pl` on a set of SAM/BAM files (set the variables `SAMs` and `ASSEMBLY`). The final set of SAM/BAM files is specified in the INI file as the parameter `SAM_FILES`, which names the files, and `SAM_DIR`, which names the directory they are in.
We have included the scripts `PreprocessSAMs.pl` and `PreprocessSAMs.sh`, which perform the filtering methods we used. `PreprocessSAMs.pl` removes all reads that do not map within 500bp of a restriction enzyme site, following the suggestion of [Yaffe & Tanay (Nature Genetics, 2011)](https://doi.org/10.1038/ng.947). To do this, it uses the script `make_BED_around_RE_site.pl` (also included) and also the bedtools library. `PreprocessSAMs.pl` also removes unpaired reads, which LACHESIS cannot use. Make sure to set the variable `$RE_site` in `PreprocessSAMs.pl`. You can also use the script `PreprocessSAMs.sh` as a batch script to run `PreprocessSAMs.pl` on a set of SAM/BAM files (set the variables `SAMs` and `ASSEMBLY`). The final set of SAM/BAM files is specified in the INI file as the parameter `SAM_FILES`, which names the files, and `SAM_DIR`, which names the directory they are in.

#### 5. Aligning the draft assembly to the reference assembly, if there is one

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