From 318626696c71a36b81e01f365c1705180de49366 Mon Sep 17 00:00:00 2001 From: XXhaos Date: Thu, 14 May 2026 10:36:24 +0900 Subject: [PATCH] =?UTF-8?q?=E4=B8=8A=E4=BC=A0=E6=96=87=E4=BB=B6=E8=87=B3?= =?UTF-8?q?=E3=80=8C/=E3=80=8D?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- M&M-意见3-AND-Results-意见5-Q4合并回答.md | 20 ++++++++------------ 1 file changed, 8 insertions(+), 12 deletions(-) diff --git a/M&M-意见3-AND-Results-意见5-Q4合并回答.md b/M&M-意见3-AND-Results-意见5-Q4合并回答.md index 163827d..d8f6b44 100644 --- a/M&M-意见3-AND-Results-意见5-Q4合并回答.md +++ b/M&M-意见3-AND-Results-意见5-Q4合并回答.md @@ -94,27 +94,23 @@ Most notably, on the SRR554369 dataset, FastqCA increases N50 by approximately 1 `FastqCA.tex` **line 754–756**（Section 3.4 收尾段，"On the high-repeat, high-GC dataset SRR554369..."一段）。 -### 5.2 原文（英文 LaTeX） +### 5.2 原文问题（仅供作者定位，**不写入论文**） -```latex -On the high-repeat, high-GC dataset SRR554369, the N50 value and the number of structurally significant contigs ($\ge$ 10 kbp) increased by approximately 10.4\% and 25.5\%, respectively, relative to the uncompressed baseline. -These properties make FastqCA directly applicable to scenarios that are highly sensitive to assembly contiguity, such as pathogen strain typing, antimicrobial resistance (AMR) island identification, and tumor exome capture, balancing high compression efficiency with robust assembly reliability. -In particular, its observed N50 (3,827 bp) and recovery of long fragments (64 contigs $\ge$ 10 kbp) are competitive within its peer group, outperforming Scalce and FQZcomp. -``` +原段落的问题不是数值本身，而是把 SRR554369 的组装指标进一步外推到具体应用场景，并使用了较强的竞争性结论。修改时应保留 Table~\ref{tab:merged_stats} 中已经报告的组装统计事实，删去未由本文实验直接支持的应用场景和机制性解释。 ### 5.3 修改后（英文 LaTeX） ```latex -\hl{On the high-repeat, high-GC dataset SRR554369, the assembly obtained from FastqCA-decompressed reads remains close to the uncompressed baseline in total length and ambiguous-base rate, while the continuity and long-contig metrics are reported alongside the other lossy-compression outputs in Table~\ref{tab:merged_stats}. Together with the compression results above, these assembly statistics characterize Q4 mode as a storage-saving setting with assembly-level metrics comparable to those obtained from the original FASTQ file.} +\hl{On the high-repeat, high-GC dataset SRR554369, the assembly obtained from FastqCA-decompressed reads has a total length and ambiguous-base rate close to the uncompressed baseline. The corresponding N50, L50, largest-contig and contig-count values are reported in Table~\ref{tab:merged_stats}, together with the original FASTQ file and the other lossy-compressed inputs. Together with the compression ratios above, these results indicate that the Q4 mode reduces storage while retaining assembly-level statistics comparable to the original FASTQ file in this benchmark.} ``` ### 5.4 中英文对照（仅供作者审阅，**不写入论文**） -| 原文（英文，line 754–756） | 修改后（英文） | 中文译文 | -|---|---|---| -| On the high-repeat, high-GC dataset SRR554369, the N50 value and the number of structurally significant contigs ($\ge$ 10 kbp) increased by approximately 10.4\% and 25.5\%, respectively, relative to the uncompressed baseline. These properties make FastqCA directly applicable to scenarios that are highly sensitive to assembly contiguity, such as pathogen strain typing, antimicrobial resistance (AMR) island identification, and tumor exome capture, balancing high compression efficiency with robust assembly reliability. In particular, its observed N50 (3,827 bp) and recovery of long fragments (64 contigs $\ge$ 10 kbp) are competitive within its peer group, outperforming Scalce and FQZcomp. | On the high-repeat, high-GC dataset SRR554369, the assembly obtained from FastqCA-decompressed reads remains close to the uncompressed baseline in total length and ambiguous-base rate, while the continuity and long-contig metrics are reported alongside the other lossy-compression outputs in Table~\ref{tab:merged_stats}. Together with the compression results above, these assembly statistics characterize Q4 mode as a storage-saving setting with assembly-level metrics comparable to those obtained from the original FASTQ file. | 在高重复、高 GC 的 SRR554369 数据集上，FastqCA 解压 reads 所得组装在总长度与模糊碱基率上接近未压缩基线；连续性指标与长 contig 指标则与其他有损压缩输出一并见 Table~\ref{tab:merged_stats}。结合上文压缩结果，这些组装统计显示，Q4 模式可作为一种节省存储的设置，其组装层面指标与原始 FASTQ 文件所得结果相当。 | +| 修改后（英文） | 中文译文 | +|---|---| +| On the high-repeat, high-GC dataset SRR554369, the assembly obtained from FastqCA-decompressed reads has a total length and ambiguous-base rate close to the uncompressed baseline. The corresponding N50, L50, largest-contig and contig-count values are reported in Table~\ref{tab:merged_stats}, together with the original FASTQ file and the other lossy-compressed inputs. Together with the compression ratios above, these results indicate that the Q4 mode reduces storage while retaining assembly-level statistics comparable to the original FASTQ file in this benchmark. | 在高重复、高 GC 的 SRR554369 数据集上，FastqCA 解压 reads 所得组装的总长度与模糊碱基率接近未压缩基线。相应的 N50、L50、最大 contig 与 contig 计数见 Table~\ref{tab:merged_stats}，并与原始 FASTQ 文件及其他有损压缩输入一并报告。结合上文压缩率结果，这些结果表明，在该基准中 Q4 模式能够减少存储，同时保留与原始 FASTQ 文件相当的组装层面统计量。 | -> 说明：这一处删去了应用场景延伸和"outperforming Scalce and FQZcomp"的重复强调，只保留 SRR554369 在组装统计上的概括性结果，并把详细数值交给 Table~\ref{tab:merged_stats}。 +> 说明：这一处删去了应用场景延伸、机制性解释和竞争性排名式表述，只保留 SRR554369 在组装统计上的概括性结果，并把详细数值交给 Table~\ref{tab:merged_stats}。 --- @@ -182,4 +178,4 @@ In particular, its observed N50 (3,827 bp) and recovery of long fragments (64 co - [x] 3 篇学术文献（Yu 2015 + Ochoa 2017 + Rivara-Espasandín 2022）贯穿三处修改，互相加强。 - [x] 已将 N50 解读从"low-pass filter / suppressing spurious errors"改为保守的结果解释：Q4 模式在本评估中保持了与原始 FASTQ 可比的组装层面指标，详细数值见 Table~\ref{tab:merged_stats}。 - [x] 已说明为何**第一轮不补 sensitivity analysis**，并备好 response letter 的措辞。 -- [x] 已修剪 "outperforming Scalce and FQZcomp" 等容易召唤"为什么不和 SPRING 比"的措辞。 +- [x] 已修剪竞争性排名式表述，避免引出与 SPRING 比较无关的额外问题。