diff --git a/paper/paper.md b/paper/paper.md index c48080f2c994d54c1f6bc1c25e774a7380ad2293..8dca059e2898fd8c5cff05cf6a9760889c094705 100644 --- a/paper/paper.md +++ b/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. $<\!$ 100 bps) and unpaired HTSRs, a total of 4,973,401 PE HTSRs remained (2,756,008,939 bps, average length $\ell\! =\!$ 277 bps), corresponding to a coverage depth of ~722$\times$. -To reduce this high coverage depth to $c \! = \!$ 50$\times$, `ROCK` (v1.9.5) was run with $k \! =\!$ 25 and $\kappa\! =\! c / \varepsilon\! \approx\!$ 45. +To reduce this high coverage depth to $c \! = \!$ 50$\times$, `ROCK` (v1.9.6) was run with $k \! =\!$ 25 and $\kappa\! =\! c / \varepsilon\! \approx\!$ 45. To assess the optimal CMS size $\lambda$, the total number $n \! =\!$ 105,584,331 of distinct canonical _k_-mers was estimated using `ntCard` [@Mohamadi:2017], and next specified to `ROCK`, leading to $\lambda\! =\!$ 1. In theory, using $\kappa\! =\!$ 45 is expected to yield a subset of $cl/(2\ell)\! \approx\!$ 344,000 PE HTSRs totaling $cl \! \approx\!$ 191 Mbps. Obtained results are summarized in Table \ref{Table 1}. @@ -117,15 +117,15 @@ Table: Running times (min:sec), and numbers of PE HTSRs and corresponding base p -------------------------------------------------------------------- $~$ **run. time** **no. PE HTSRs** **no. bps** ------------------- --------------- ------------------ ------------- - $\kappa'\! =\!$ 0 3:09 425,856 242,772,228 + $\kappa'\! =\!$ 0 3:16 424,040 244,188,971 - $\kappa'\! =\!$ 2 3:23 388,223 225,527,243 + $\kappa'\! =\!$ 2 3:22 386,665 227,069,995 - $\kappa'\! =\!$ 4 3:23 373,643 218,820,128 + $\kappa'\! =\!$ 4 3:23 371,834 220,241,468 - $\kappa'\! =\!$ 6 3:24 372,186 218,209,793 + $\kappa'\! =\!$ 6 3:24 370,336 219,612,591 - $\kappa'\! =\!$ 8 3:24 371,843 218,067,593 + $\kappa'\! =\!$ 8 3:24 369,994 219,471,025 -------------------------------------------------------------------- For comparison sake, comparable standard digital normalizations ($\kappa\! =\!$ 45 and $k \! =\!$ 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).