Genome-assessment-post-assembly
Version 1 (earliest)

Version 2 (latest)

Version 1 (earliest)

Workflow Type: Galaxy

Post-genome assembly quality control workflow using Quast, BUSCO, Meryl, Merqury and Fasta Statistics. Updates November 2023. Inputs: reads as fastqsanger.gz (not fastq.gz), and assembly.fasta. New default settings for BUSCO: lineage = eukaryota; for Quast: lineage = eukaryotes, genome = large. Reports assembly stats into a table called metrics.tsv, including selected metrics from Fasta Stats, and read coverage; reports BUSCO versions and dependencies; and displays these tables in the workflow report. Note: a known bug is that sometimes the workflow report text resets to default text. To restore, look for an earlier workflow version with correct workflow report text, and copy and paste report text into current version.

SEEK ID: https://workflowhub.eu/workflows/794?version=1

Inputs

ID	Name	Description	Type
FASTA contigs - Primary Assembly	#main/FASTA contigs - Primary Assembly	n/a	File
Raw reads	#main/Raw reads	n/a	File

Steps

ID	Name	Description
2	FASTQ to FASTA	toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5
3	Meryl	toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
4	Fasta Statistics	toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0
5	Quast	toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy1
6	Busco	toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0
7	Fasta Statistics	toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0
8	Merqury	toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3
9	Search in textfiles	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
10	Relabel some items in Fasta stats	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1
11	Get required Busco stats	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
12	Get Busco version	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
13	Get Busco dependencies	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
14	Search in textfiles	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
15	Cut	Cut1
16	Filter out unneeded lines from fasta stats	toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.0
17	Rename some items and add in delimiters for later	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1
18	Reformat some text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1
19	Cut	Cut1
20	Extract assembly size	toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.0
21	Extract number of contigs	toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.0
22	Extract Contig N and L 50s and 90s	toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.0
23	Extract longest contig	toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.0
24	Extract GC content	toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.0
25	Convert commas to tabs	Convert characters1
26	Collate Busco info	cat1
27	Paste	Paste1
28	Add blank header	toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0
29	Transpose cols to rows	toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0
30	Convert to table	Convert characters1
31	Compute coverage, total reads length divided by assembly length	toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0
32	Convert underscores to tabs	Convert characters1
33	Keep two columns	Cut1
34	Round the percentage to 2 decimal places	toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0
35	Label the column	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3
36	Join info into one table	cat1

Outputs

ID	Name	Description	Type
Busco and dependencies version	#main/Busco and dependencies version	n/a	File
Busco on input dataset(s): full table	#main/Busco on input dataset(s): full table	n/a	File
Fasta Statistics on input dataset(s): summary stats	#main/Fasta Statistics on input dataset(s): summary stats	n/a	File
Genome assembly metrics	#main/Genome assembly metrics	n/a	File
Genome coverage	#main/Genome coverage	n/a	File
Merqury on input dataset(s): bed	#main/Merqury on input dataset(s): bed	n/a	File
Merqury on input dataset(s): png	#main/Merqury on input dataset(s): png	n/a	File
Merqury on input dataset(s): qv	#main/Merqury on input dataset(s): qv	n/a	File
Merqury on input dataset(s): size files	#main/Merqury on input dataset(s): size files	n/a	File
Merqury on input dataset(s): stats	#main/Merqury on input dataset(s): stats	n/a	File
Merqury on input dataset(s): wig	#main/Merqury on input dataset(s): wig	n/a	File
Meryl on input dataset(s): read-db.meryldb	#main/Meryl on input dataset(s): read-db.meryldb	n/a	File
Quast on input dataset(s): HTML report	#main/Quast on input dataset(s): HTML report	n/a	File
Quast on input dataset(s): PDF report	#main/Quast on input dataset(s): PDF report	n/a	File
Quast on input dataset(s): Log	#main/Quast on input dataset(s): Log	n/a	File
Quast on input dataset(s): tabular report	#main/Quast on input dataset(s): tabular report	n/a	File
_anonymous_output_1	#main/_anonymous_output_1	n/a	File
_anonymous_output_10	#main/_anonymous_output_10	n/a	File
_anonymous_output_11	#main/_anonymous_output_11	n/a	File
_anonymous_output_12	#main/_anonymous_output_12	n/a	File
_anonymous_output_13	#main/_anonymous_output_13	n/a	File
_anonymous_output_14	#main/_anonymous_output_14	n/a	File
_anonymous_output_15	#main/_anonymous_output_15	n/a	File
_anonymous_output_16	#main/_anonymous_output_16	n/a	File
_anonymous_output_17	#main/_anonymous_output_17	n/a	File
_anonymous_output_18	#main/_anonymous_output_18	n/a	File
_anonymous_output_19	#main/_anonymous_output_19	n/a	File
_anonymous_output_2	#main/_anonymous_output_2	n/a	File
_anonymous_output_20	#main/_anonymous_output_20	n/a	File
_anonymous_output_21	#main/_anonymous_output_21	n/a	File
_anonymous_output_22	#main/_anonymous_output_22	n/a	File
_anonymous_output_23	#main/_anonymous_output_23	n/a	File
_anonymous_output_24	#main/_anonymous_output_24	n/a	File
_anonymous_output_25	#main/_anonymous_output_25	n/a	File
_anonymous_output_26	#main/_anonymous_output_26	n/a	File
_anonymous_output_3	#main/_anonymous_output_3	n/a	File
_anonymous_output_4	#main/_anonymous_output_4	n/a	File
_anonymous_output_5	#main/_anonymous_output_5	n/a	File
_anonymous_output_6	#main/_anonymous_output_6	n/a	File
_anonymous_output_7	#main/_anonymous_output_7	n/a	File
_anonymous_output_8	#main/_anonymous_output_8	n/a	File
_anonymous_output_9	#main/_anonymous_output_9	n/a	File
out_file1	#main/out_file1	n/a	File
outfile	#main/outfile	n/a	File