diff --git a/README.md b/README.md index 348ce99..112e5ed 100644 --- a/README.md +++ b/README.md @@ -5,9 +5,9 @@ cd wtdbg2 && make # assemble PacBio reads ./wtdbg2 -t 16 -i pacbio.fa.gz -fo prefix -L 5000 # assemble Nanopore reads -./wtdbg2 -t 16 -i ont.fa.gz -fo prefix +./wtdbg2 -t 16 -i ont.fa.gz -fo prefix -L 5000 # derive consensus -./wtpoa-cns -t 16 -i prefix.ctg.lay > prefix.ctg.lay.fa +./wtpoa-cns -t 16 -i prefix.ctg.lay -fo prefix.ctg.lay.fa ``` ## Introduction @@ -41,7 +41,7 @@ produces the final consensus in FASTA. A typical workflow looks like this: ./wtpoa-cns -t 16 -i prefix.ctg.lay -fo prefix.ctg.lay.fa ``` where `-t` specifies the number of CPU cores (`-t 0` to use all processors). When the default doesn't work -well, you may need to apply more options. +well, you may need to apply more options. See [README-ori.md][readme-ori] for more help. Wtdbg2 combines normal k-mers and homopolymer-compressed (HPC) k-mers to find read overlaps. Option `-k` specifies the length of normal k-mers, while `-p` @@ -58,7 +58,7 @@ the assembly step (not including the consensus step): |Dataset |Genome|Coverage |Wtdbg2 options|CPU hours|Peak RAM| |:-----------------------|-----:|---------:|:-------------|--------:|-------:| |[E. coli][pbcr] |4.6Mb |PacBio x20| | | | -|[C. elegans][ce] |100Mb |PacBio x80| | | | +|[C. elegans][ce] |100Mb |PacBio x80|-L5000 -e4 |3.3 | 9.7G| |[Human CHM1][chm1] |3Gb |PacBio x60|-L5000 -e4 |378.5 | 252.7G| |[Human NA12878][na12878]|3Gb |ONT x30 |-S2 -e2 |197.4 | 244.9G| |[Axolotl][axosra] |32Gb |PacBio x32|-L5000 -AS2 |3189.7 | 1593.6G| @@ -76,6 +76,7 @@ the assembly step (not including the consensus step): Please use the [GitHub's Issues page][issue] if you have questions. You may also directly contact Jue Ruan at ruanjue@gmail.com. +[readme-ori]: https://github.com/ruanjue/wtdbg2/README-ori.md [miniasm]: https://github.com/lh3/miniasm [canu]: https://github.com/marbl/canu [falcon]: https://github.com/PacificBiosciences/FALCON