From f6ec19e41632f36bb441a2ce6a574632a94694ed Mon Sep 17 00:00:00 2001 From: Mikhail Kolmogorov Date: Sat, 21 Aug 2021 11:21:34 -0700 Subject: [PATCH] typos --- docs/FAQ.md | 7 +++---- docs/USAGE.md | 12 ++++++------ flye/main.py | 4 ++-- 3 files changed, 11 insertions(+), 12 deletions(-) diff --git a/docs/FAQ.md b/docs/FAQ.md index 7d5eade68..c9e5558a9 100644 --- a/docs/FAQ.md +++ b/docs/FAQ.md @@ -43,7 +43,7 @@ many human assemblies, which typically require ~450Gb of RAM for ONT and ~140Gb Memory consumption grows linearly with genome size and reads coverage. Thus, genomes beyond ~10Gb is size might be problemmatic to assmeble. -Typically, memory requirements are lower for higher quality data (e.g. PacBio HiFi or ONT Hq mode). +Typically, memory requirements are lower for higher quality data (e.g. PacBio HiFi or ONT HQ mode). Are PacBio CCS/HiFi reads supported? ------------------------------- @@ -175,13 +175,12 @@ Do I still need Illumina polishing or long-read polishing is good enough? It is a somewhat difficult question to answer. Flye does include polishing step, and it producing high quality consensus on bacterial -PacBio datasets with high coverage. For example, see this recent +PacBio CLR datasets with high coverage. For example, see this recent [evaluation by Ryan Wick](https://github.com/rrwick/Long-read-assembler-comparison). On the other hand, PacBio has specialized Quiver/Arrow tools that are more advanced, since they use PacBio-specific signal information. -It is possible, that you can get a bit of improvement after applying these tools. -For the recent ONT data (Guppy4+), Flye often achieves Q30+ quality on verious genomes. +For the recent ONT data (Guppy4+), Flye often achieves Q30+ quality on various genomes. One can typically push that a bit higher using Medaka or Nanopolish. See the recent [Trycycler paper and tool](https://github.com/rrwick/Trycycler) for the discussion. diff --git a/docs/USAGE.md b/docs/USAGE.md index 15a3b908e..b5f89df8c 100644 --- a/docs/USAGE.md +++ b/docs/USAGE.md @@ -77,20 +77,20 @@ optional arguments: Input reads can be in FASTA or FASTQ format, uncompressed or compressed with gz. Currently, PacBio (CLR, HiFi, corrected) -and ONT reads (raw, HQ, corrected) are supported. Expected error rates are -<20% for CLR/raw ONT, <5% for ONT HQ, <3% for corrected, and <1% for HiFi. Note that Flye +and ONT reads (regular, HQ, corrected) are supported. Expected error rates are +<20% for PB CLR/regular ONT, <5% for ONT HQ, <3% for corrected, and <1% for HiFi. Note that Flye was primarily developed to run on uncorrected reads. You may specify multiple files with reads (separated by spaces). Mixing different read -types is not yet supported. The --meta option enables the mode +types is not yet supported. The `--meta` option enables the mode for metagenome/uneven coverage assembly. To reduce memory consumption for large genome assemblies, you can use a subset of the longest reads for initial disjointig -assembly by specifying --asm-coverage and --genome-size options. Typically, +assembly by specifying `--asm-coverage` and `--genome-size` options. Typically, 40x coverage is enough to produce good disjointigs. You can run Flye polisher as a standalone tool using ---polish-target option. +`--polish-target` option. ## Examples @@ -238,7 +238,7 @@ all reads will be used at the later pipeline stages (e.g. for repeat resolution) ### Running only Flye polisher To polish an existing assembly, you can run Flye polisher as a standalone tool -using --polish-target. Paths to reads are specified similarly to the assembly mode, +using `--polish-target`. Paths to reads are specified similarly to the assembly mode, and bam file could also be proveded instead of reads (the mapping stage in this case will be skipped). diff --git a/flye/main.py b/flye/main.py index 01308ca7b..c84fc5666 100644 --- a/flye/main.py +++ b/flye/main.py @@ -625,8 +625,8 @@ def _usage(): def _epilog(): return ("Input reads can be in FASTA or FASTQ format, uncompressed\n" "or compressed with gz. Currently, PacBio (CLR, HiFi, corrected)\n" - "and ONT reads (raw, HQ, corrected) are supported. Expected error rates are\n" - "<20% for CLR/raw ONT, <5% for ONT HQ, <3% for corrected, and <1% for HiFi. Note that Flye\n" + "and ONT reads (regular, HQ, corrected) are supported. Expected error rates are\n" + "<15% for PB CLR/regular ONT; <5% for ONT HQ, <3% for corrected, and <1% for HiFi. Note that Flye\n" "was primarily developed to run on uncorrected reads. You may specify multiple\n" "files with reads (separated by spaces). Mixing different read\n" "types is not yet supported. The --meta option enables the mode\n"