diff --git a/tools/spades/biosyntheticspades.xml b/tools/spades/biosyntheticspades.xml index 2aadc91878a..46c5c7e2e9c 100644 --- a/tools/spades/biosyntheticspades.xml +++ b/tools/spades/biosyntheticspades.xml @@ -16,6 +16,7 @@ #end if @PREPROCESS_NANOPORE_PACBIO_FILES@ +@OMP_THREADS@ ## run spades.py --bio -o 'output' @@ -175,7 +176,7 @@ A detailed description can be found in the `output section `_ and on the `project website `_. +More information can be found on `github `_. ]]> 10.1101/gr.243477.118 diff --git a/tools/spades/coronaspades.xml b/tools/spades/coronaspades.xml index 60a9d4dd7af..d670a74112e 100644 --- a/tools/spades/coronaspades.xml +++ b/tools/spades/coronaspades.xml @@ -19,6 +19,7 @@ @PREPROCESS_SANGER_FILES@ +@OMP_THREADS@ ## run coronaspades.py -o 'output' @@ -162,7 +163,7 @@ Input data can be provided as interlaced, forward and reverse, merged and unpair **References** -More information can be found on `github `_ and on the `project website `_. +More information can be found on `github `_. ]]> 10.1093/bioinformatics/btab597 diff --git a/tools/spades/macros.xml b/tools/spades/macros.xml index f5b31fae725..b635f84a742 100644 --- a/tools/spades/macros.xml +++ b/tools/spades/macros.xml @@ -1,6 +1,6 @@ 3.15.4 - 1 + 2 spades @@ -43,6 +43,9 @@ + @@ -738,7 +741,7 @@ A detailed description can be found in the `input section `_ (e.g. assemble using k-mer lengths 21,33,55,77,99,127). However, due to increased error rate some changes of k-mer lengths (e.g. selection of shorter ones) may be required. For example, if you ran SPAdes with k-mer lengths 21,33,55,77 and then decided to assemble the same data set using more iterations and larger values of K, you can run SPAdes once again specifying the same output folder and the following options: --restart-from k77 -k 21,33,55,77,99,127 --mismatch-correction -o . Do not forget to copy contigs and scaffolds from the previous run. We're planning to tackle issue of selecting k-mer lengths for IonTorrent reads in next versions. +The selection of k-mer length is non-trivial for IonTorrent. If the dataset is more or less conventional (good coverage, not high GC, etc), then use our `recommendation for long reads `_ (e.g. assemble using k-mer lengths 21,33,55,77,99,127). However, due to increased error rate some changes of k-mer lengths (e.g. selection of shorter ones) may be required. For example, if you ran SPAdes with k-mer lengths 21,33,55,77 and then decided to assemble the same data set using more iterations and larger values of K, you can run SPAdes once again specifying the same output folder and the following options: --restart-from k77 -k 21,33,55,77,99,127 --mismatch-correction -o . Do not forget to copy contigs and scaffolds from the previous run. We're planning to tackle issue of selecting k-mer lengths for IonTorrent reads in next versions. You may need no error correction for Hi-Q enzyme at all. However, we suggest trying to assemble your data with and without error correction and select the best variant. diff --git a/tools/spades/metaplasmidspades.xml b/tools/spades/metaplasmidspades.xml index 7ffc41264f6..e232e3c79cd 100644 --- a/tools/spades/metaplasmidspades.xml +++ b/tools/spades/metaplasmidspades.xml @@ -19,6 +19,7 @@ @PREPROCESS_CONTIGS_FILES@ @PREPROCESS_ASSEMBLY_GRAPH_FILES@ +@OMP_THREADS@ ## run spades.py --meta --plasmid -o 'output' @@ -233,7 +234,7 @@ metaplasmidSPAdes is a subtool for assembling plasmids from metagenomic data set **References** -More information can be found on `github `_ and on the `project website `_. +More information can be found on `github `_. ]]> 10.1101/gr.241299.118 diff --git a/tools/spades/metaspades.xml b/tools/spades/metaspades.xml index 70f8240bff0..af05e559d94 100755 --- a/tools/spades/metaspades.xml +++ b/tools/spades/metaspades.xml @@ -16,6 +16,7 @@ #end if @PREPROCESS_NANOPORE_PACBIO_FILES@ +@OMP_THREADS@ ## run metaspades.py -o 'output' @@ -185,7 +186,7 @@ metaSPAdes is a subtool for assembling metagenomic data sets. **References** -More information can be found on `github `_ and on the `project website `_. +More information can be found on `github `_. ]]> 10.1101/gr.213959.116 diff --git a/tools/spades/metaviralspades.xml b/tools/spades/metaviralspades.xml index a0cb488c6d0..b8819fba75d 100644 --- a/tools/spades/metaviralspades.xml +++ b/tools/spades/metaviralspades.xml @@ -19,6 +19,7 @@ @PREPROCESS_CONTIGS_FILES@ @PREPROCESS_ASSEMBLY_GRAPH_FILES@ +@OMP_THREADS@ ## run spades.py --metaviral -o 'output' @@ -233,7 +234,7 @@ metaplasmidSPAdes is a subtool for assembling plasmids from metagenomic data set **References** -More information can be found on `github `_ and on the `project website `_. +More information can be found on `github `_. ]]> 10.1101/gr.241299.118 diff --git a/tools/spades/plasmidspades.xml b/tools/spades/plasmidspades.xml index 3685ae9e73d..9b33eb2a654 100644 --- a/tools/spades/plasmidspades.xml +++ b/tools/spades/plasmidspades.xml @@ -19,6 +19,7 @@ @PREPROCESS_CONTIGS_FILES@ @PREPROCESS_ASSEMBLY_GRAPH_FILES@ +@OMP_THREADS@ ## run plasmidspades.py $operation_mode @@ -377,7 +378,7 @@ plasmidSPAdes is a subtool for assembling plasmid data sets. **References** -More information can be found on `github `_ and on the `project website `_. +More information can be found on `github `_. ]]> 10.1093/bioinformatics/btw493 diff --git a/tools/spades/rnaspades.xml b/tools/spades/rnaspades.xml index 3e254ba5883..79fd4937968 100644 --- a/tools/spades/rnaspades.xml +++ b/tools/spades/rnaspades.xml @@ -18,7 +18,7 @@ @PREPROCESS_CONTIGS_FILES@ @PREPROCESS_FL_RNA_FILES@ - +@OMP_THREADS@ ## run rnaspades.py -o 'output' @@ -238,7 +238,7 @@ and strand-specificity. Transcript quantification for each sample can be done af **References** -More information can be found on on `github `_ and on the `project website `_. +More information can be found on on `github `_. ]]> 10.1101/420208 diff --git a/tools/spades/rnaviralspades.xml b/tools/spades/rnaviralspades.xml index 1a8ccd80e48..e6ecb2cb977 100644 --- a/tools/spades/rnaviralspades.xml +++ b/tools/spades/rnaviralspades.xml @@ -18,6 +18,7 @@ @PREPROCESS_CONTIGS_FILES@ @PREPROCESS_SANGER_FILES@ +@OMP_THREADS@ ## run spades.py --rnaviral -o 'output' @@ -351,7 +352,7 @@ rnaviralSPAdes is a pipeline specially designed for de novo assembler tailored f **References** -More information are available on `github `_ and on the `project website `_. +More information are available on `github `_. ]]> diff --git a/tools/spades/spades.xml b/tools/spades/spades.xml index 7759e818d92..23bb09761a5 100644 --- a/tools/spades/spades.xml +++ b/tools/spades/spades.xml @@ -18,6 +18,7 @@ @PREPROCESS_CONTIGS_FILES@ @PREPROCESS_SANGER_FILES@ +@OMP_THREADS@ ## run spades.py $operation_mode @@ -731,7 +732,7 @@ spades.py **References** -More information are available on `github `_ and on the `project website `_. +More information are available on `github `_. ]]> 10.1089/cmb.2012.0021