If the installation is successful, you will find the following information at the end of the log:
<spades installation dir>/dipspades.py --test
* Assembled consensus contigs are in: test_dipspades/dipspades/consensus_contigs.fasta * Assembled paired consensus contigs are in: test_dipspades/dipspades/paired_consensus_contigs.fasta * Assembled paired consensus contigs are in: test_dipspades/dipspades/unpaired_consensus_contigs.fasta * Alignment of haplocontigs is in: test_dipspades/dipspades/haplocontigs_alignent * Assembled paired consensus contigs are in: test_dipspades/dipspades/haplotype_assembly.out * Possibly conservative regions are in: test_dipspades/dipspades/possibly_conservative_regions.fasta Thank you for using SPAdes! ======= dipSPAdes finished. dipSPAdes log can be found here: test_dipspades/dipspades/dipspades.log
dipspades.py [options] -o <output_dir>
PATHvariable (provide full path to dipSPAdes executable otherwise:
<spades installation dir>/dipspades.py).
Specifies the output directory. Required option.
Runs SPAdes on the toy data set; see section 2.
Specifies file with haplocontigs in FASTA format. Note that dipSPAdes can use any number of haplocontig files.
Indicates significant amount of expected gaps in genome coverage (e.g. for datasets with relatively low coverage).
Indicates extreme heterozygosity rate in haplomes (e.g. haplomes differ by long insertions/deletions).
Enables haplotype assembly phase that results in files haplotype_assembly.out, conservative_regions.fasta, and possibly_conservative_regions.fasta (see Haplotype assembly output).
To perform assembly (construct consensus contigs and perform haplotype assembly) of diploid genome from preliminary computed haplocontigs (
dipspades.py -1 reads_left.fastq -2 reads_right.fastq -o output_dir
To perform assembly of diploid genome from both reads (
dipspades.py --hap haplocontigs1.fasta --hap haplocontigs2.fasta -o output_dir
reads_right.fastq) and preliminary computed haplocontigs (
dipspades.py -1 reads_left.fastq -2 reads_right.fastq --hap haplocontigs.fasta -o output_dir
To relaunch steps 2 and 3 of dipSPAdes (see dipSPAdes pipeline section) with different set of advanced options you can use haplocontigs constructed in the previous run (see dipSPAdes output section) run:
dipspades.py -1 reads_left.fastq -2 reads_right.fastq --expect-gaps -o output_dir
dipspades.py -hap output_dir/haplocontigs.fasta --expect-gaps --expect-rearrangements --hap-assembly -o new_output_dir
Each block corresponds to alignment of haplocontigs to consensus contigs
Consensus contig: CONSENSUS_CONTIG_NAME Overlapping haplocontigs: HAPLOCONTIG_NAME_1 HAPLOCONTIG_NAME_2 ... Nested haplocontigs: HAPLOCONTIG_NAME_3 HAPLOCONTIG_NAME_4 ...
CONSENSUS_CONTIG_NAME. Name of consensus contig,
CONSENSUS_CONTIG_NAME, coincides with the name in file consensus_contigs.fasta. Further the list of pairs of haplocontig names is printed. Haplocontigs in each pair at least partially correspond either to the same positions on the same haplome or to homologous positions on different haplomes. Also the list is divided into two subblocks:
Overlapping haplocontigscontain pairs of haplocontigs such that the suffix of the first haplocontig corresponds to the prefix of the second contig.
Nested haplocontigscontains pairs of haplocontigs such that certain subcontig of the second contig corresponds to the entire first contig.
HAPLOCONTIG_NAME_2are names of homologous haplocontigs that correspond to different haplomes and at least partially correspond to homologous positions in different chromosomes. Names correspond to the names of haplocontigs specified as an input using options
--hapor computed at the first step.
If you use dipSPAdes in your research, please include Safonova, Bankevich, and Pevzner, 2014 in your reference list.
In addition, we would like to list your publications that use our software on our website. Please email the reference, the name of your lab, department and institution to firstname.lastname@example.org.