MC_COVID19like_Assembly_Reads
Version 1

Work-in-progress

This WF is based on the official Covid19-Galaxy assembly workflow as available from https://covid19.galaxyproject.org/genomics/2-assembly/ . It has been adapted to suit the needs of the analysis of metagenomics sequencing data. Prior to be submitted to INDSC databases, these data need to be cleaned from contaminant reads, including reads of possible human origin.

The assembly of the SARS-CoV-2 genome is performed using both the Unicycler and the SPAdes assemblers, similar to the original WV.

To facilitate the deposition of raw sequencing reads in INDSC databases, different fastq files are saved during the different steps of the WV. Which reflect different levels of stringency/filtration:

(1) Initially fastq are filtered to remove human reads.

(2) Subsequently, a similarity search is performed against the reference assembly of the SARS-CoV-2 genome, to retain only SARS-CoV-2 like reads.

(3) Finally, SARS-CoV-2 reads are assembled, and the bowtie2 program is used to identify (and save in the corresponding fastq files) only reads that are completely identical to the final assembly of the genome.

Any of the fastq files produced in (1), (2) or (3) are suitable for being submitted in raw reads repositories. While the files filtered according to (1) are richer and contain more data, including for example genomic sequences of different microbes living in the oral cavity; files filtered according to (3) contain only the reads that are completely identical to the final assembly. This should guarantee that any re-analysis/re-assembly of these always produce consistent and identical results. File obtained at (2) include all the reads in the sequencing reaction that had some degree of similarity with the reference SARS-CoV-2 genome, these may include subgenomic RNAs, but also polymorphic regions/variants in the case of a coinfection by multiple SARS-CoV-2 strains. Consequently, reanalysis of these data is not guarateed to produce identical and consistent results, depending on the parameters used during the assembly. However, these data contain more information.

Please feel free to comment, ask questions and/or add suggestions

Inputs

ID Name Description Type
library library runtime parameter for tool Bowtie2 n/a
library library runtime parameter for tool Bowtie2 n/a
library library runtime parameter for tool Bowtie2 n/a
library library runtime parameter for tool Bowtie2 n/a
reference_genome reference_genome runtime parameter for tool Bowtie2 n/a
lr_align lr_align runtime parameter for tool Create assemblies with Unicycler n/a
long long runtime parameter for tool Create assemblies with Unicycler n/a
rotation rotation runtime parameter for tool Create assemblies with Unicycler n/a
pacbio_reads pacbio_reads runtime parameter for tool SPAdes n/a
nanopore_reads nanopore_reads runtime parameter for tool SPAdes n/a
trusted_contigs trusted_contigs runtime parameter for tool SPAdes n/a
untrusted_contigs untrusted_contigs runtime parameter for tool SPAdes n/a
sanger_reads sanger_reads runtime parameter for tool SPAdes n/a
library library runtime parameter for tool Bowtie2 n/a
library library runtime parameter for tool Bowtie2 n/a
reference_genome reference_genome runtime parameter for tool Bowtie2 n/a
library library runtime parameter for tool Bowtie2 n/a
library library runtime parameter for tool Bowtie2 n/a
reference_genome reference_genome runtime parameter for tool Bowtie2 n/a

Steps

ID Name Description
0 Forward reads
1 Reverse read
2 Filter_human_reads toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0
3 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1
4 Any_SARS-CoV-2_reads toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0
5 Create assemblies with Unicycler toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.6.0
6 SPAdes toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1
7 Keep_identical_reads_Unicycler toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0
8 Keep_identical_reads_SPAdes toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0

Outputs

ID Name Description Type
output_unaligned_reads_l output_unaligned_reads_l n/a fastqsanger
output_aligned_reads_l output_aligned_reads_l n/a fastqsanger
output_aligned_reads_r output_aligned_reads_r n/a fastqsanger
output_unaligned_reads_r output_unaligned_reads_r n/a fastqsanger
output output n/a bam
mapping_stats mapping_stats n/a txt
output_paired_coll output_paired_coll n/a input
out1 out1 n/a input
out2 out2 n/a input
report_html report_html n/a html
report_json report_json n/a json
output_unaligned_reads_l output_unaligned_reads_l n/a fastqsanger
output_aligned_reads_l output_aligned_reads_l n/a fastqsanger
output_aligned_reads_r output_aligned_reads_r n/a fastqsanger
output_unaligned_reads_r output_unaligned_reads_r n/a fastqsanger
output output n/a bam
mapping_stats mapping_stats n/a txt
assembly_graph assembly_graph n/a tabular
assembly assembly n/a fasta
out_contig_stats out_contig_stats n/a tabular
out_scaffold_stats out_scaffold_stats n/a tabular
out_contigs out_contigs n/a fasta
out_scaffolds out_scaffolds n/a fasta
out_log out_log n/a txt
contig_graph contig_graph n/a txt
scaffold_graph scaffold_graph n/a txt
output_unaligned_reads_l output_unaligned_reads_l n/a fastqsanger
output_aligned_reads_l output_aligned_reads_l n/a fastqsanger
output_aligned_reads_r output_aligned_reads_r n/a fastqsanger
output_unaligned_reads_r output_unaligned_reads_r n/a fastqsanger
output output n/a bam
mapping_stats mapping_stats n/a txt
output_unaligned_reads_l output_unaligned_reads_l n/a fastqsanger
output_aligned_reads_l output_aligned_reads_l n/a fastqsanger
output_aligned_reads_r output_aligned_reads_r n/a fastqsanger
output_unaligned_reads_r output_unaligned_reads_r n/a fastqsanger
output output n/a bam
mapping_stats mapping_stats n/a txt
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Created: 4th Nov 2020 at 18:35

Last updated: 5th Nov 2020 at 07:42

Last used: 24th Nov 2020 at 03:38

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