diff --git a/README.md b/README.md index b79697f..57df2b4 100644 --- a/README.md +++ b/README.md @@ -55,7 +55,8 @@ k-mers by their hashcodes. For data of relatively low coverage, you may increase this sampling rate by reducing `-S`. This will greatly increase the peak memory as a cost, though. Option `-e`, which defaults to 3, specifies the minimum read coverage of an edge in the assembly graph. You may adjust this -option according to the overall sequencing depth, too. For PacBio data, +option according to the overall sequencing depth, too. Option `-A` also helps +relatively low coverage data at the cost of performance. For PacBio data, `-L5000` often leads to better assemblies emperically, so is recommended. Please run `wtdbg2 --help` for a complete list of available options or consult [README-ori.md](README-ori.md) for more help. @@ -63,19 +64,19 @@ Please run `wtdbg2 --help` for a complete list of available options or consult The following table shows various command lines and their resource usage for the assembly step: -|Dataset |Genome|Coverage|Asm options |CPU asm |CPU cns |Real |Peak RAM| -|:-----------------------|-----:|-------:|:------------------|-------:|-------:|------:|-------:| -|[E. coli][pbcr] |4.6Mb |PB x20 |-t32 -L5000 | 39s| 10m34s| 29s| 1.1G| -|[C. elegans][ce] |100Mb |PB x80 |-t32 -L5000 -e4 | 1h00m| 5h06m| 16m16s| 9.5G| -|[Human NA12878][na12878]|3Gb |ONT x36 |-t36 -p19 -AS2 -e2 -L5000|822h28m|115h59m|27h42m|182.1G| -|[Human NA19240][na19240]|3Gb |ONT x35 |-t32 -p19 -AS2 -e2 | 706h30m| 114h45m| 27h33m| 177.5G| -|[C. elegans][ce] |100Mb |PB x80 |-t64 -L5000 | 1h46m| 5h27m| 14m17s| 10.1G| -|[Human CHM1][chm1] |3Gb |PB x60 |-t64 -L10000 | 186h15m| 131h52m| 7h41m| 265.2G| -|[Axolotl][axosra] |32Gb |PB x32 |-t96 -L5000 -AS2 | 3189h| | | 1593.6G| - -The first four lines were assembled with 32 threads on a server with Xeon -E5-2683 CPUs at 2GHz. The rest were assembled on a server with Xeon E7-8857 -CPUs at 3GHz. +|Dataset |GSize |Cov |Asm options |CPU asm |CPU cns |Real tot| RAM| +|:-----------------------|-----:|-------:|:------------------|-------:|-------:|-------:|-------:| +|[E. coli][pbcr] |4.6Mb |PB x20 |-t32 -L5000 | 39s| 10m34s| 29s| 1.1G| +|[C. elegans][ce] |100Mb |PB x80 |-t32 -L5000 -e4 | 1h00m| 5h06m| 16m16s| 9.5G| +|[Human NA12878][na12878]|3Gb |ONT x36 |-t36 -p19 -AS2 -e2
-L5000|822h28m|115h59m|27h42m|182.1G| +|[Human NA19240][na19240]|3Gb |ONT x35 |-t32 -p19 -AS2 -e2 | 706h30m| 114h45m| 27h33m| 177.5G| +|[C. elegans][ce] |100Mb |PB x80 |-t64 -L5000 | 1h46m| 5h27m| 14m17s| 10.1G| +|[Human CHM1][chm1] |3Gb |PB x60 |-t64 -L10000 | 186h15m| 131h52m| 7h41m| 265.2G| +|[Axolotl][axosra] |32Gb |PB x32 |-t96 -L5000 -AS2 | 3189h| | | 1593.6G| + +The timing was obtained on three local servers with different hardware +configurations. There are also run-to-run fluctuations. Exact timing on your +machines may differ. ## Limitations