Update paper.md v1.9.5

paper/paper.md

@@ -107,7 +107,7 @@ To illustrate the performances of `ROCK` on a real-case high coverage WGS datase
 The two FASTQ files were first processed using `AlienTrimmer` [@Criscuolo:2013] to trim off 5'/3' regions containing many sequencing errors (i.e. Phred score cutoff $Q \! =\!$ 20) or stretches of identical nucleotides.
 After discarding too short (i.e. $<\!$&nbsp;100&nbsp;bps) and unpaired HTSRs, a total of 4,973,401&nbsp;PE HTSRs remained (2,756,008,939&nbsp;bps, average length $\ell\! =\!$&nbsp;277&nbsp;bps), corresponding to a coverage depth of ~722$\times$.
 
-To reduce this high coverage depth to $c \! = \!$&nbsp;50$\times$, `ROCK` was run with $k \! =\!$&nbsp;25 and $\kappa\! =\! c / \varepsilon\! \approx\!$&nbsp;45. 
+To reduce this high coverage depth to $c \! = \!$&nbsp;50$\times$, `ROCK` (v1.9.5) was run with $k \! =\!$&nbsp;25 and $\kappa\! =\! c / \varepsilon\! \approx\!$&nbsp;45. 
 To assess the optimal CMS size $\lambda$, the total number $n \! =\!$&nbsp;105,584,331 of distinct canonical _k_-mers was estimated using `ntCard` [@Mohamadi:2017], and next specified to `ROCK`, leading to $\lambda\! =\!$&nbsp;1. 
 In theory, using $\kappa\! =\!$&nbsp;45 is expected to yield a subset of $cl/(2\ell)\! \approx\!$&nbsp;344,000 PE HTSRs totaling $cl \! \approx\!$&nbsp;191&nbsp;Mbps.
 Obtained results are summarized in Table&nbsp;\ref{Table 1}.
@@ -117,15 +117,15 @@ Table: Running times (min:sec), and numbers of PE HTSRs and corresponding base p
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          $~$         **run. time**   **no. PE HTSRs**   **no. bps**
 ------------------- --------------- ------------------ -------------
- $\kappa'\! =\!$ 0       3:09           425,999         241,820,129 
+ $\kappa'\! =\!$ 0       3:09           425,856         242,772,228 
 
- $\kappa'\! =\!$ 2       3:23           388,162         224,479,872
+ $\kappa'\! =\!$ 2       3:23           388,223         225,527,243
 
- $\kappa'\! =\!$ 4       3:23           376,746         217,850,311
+ $\kappa'\! =\!$ 4       3:23           373,643         218,820,128
 
- $\kappa'\! =\!$ 6       3:24           372,315         217,251,626
+ $\kappa'\! =\!$ 6       3:24           372,186         218,209,793
 
- $\kappa'\! =\!$ 8       3:24           371,973         217,109,407
+ $\kappa'\! =\!$ 8       3:24           371,843         218,067,593
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 For comparison sake, comparable standard digital normalizations ($\kappa\! =\!$&nbsp;45 and $k \! =\!$&nbsp;25) were also carried out on the same computer (AMD Epyc 2.2 GHz processor, 128 Gb RAM) using other dedicated tools (see Statement of need).