Purge duplicates from hifiasm assembly v1.0 (HiFi genome assembly stage 3)
Version 1

Workflow Type: Galaxy
Stable

Optional workflow to purge duplicates from the contig assembly.

Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)

Inputs

ID Name Description Type
HiFiASM 1o assembly HiFiASM 1o assembly Primary assembly input from hifiasm workflow, in FASTA format. n/a
HiFi reads as FASTQ HiFi reads as FASTQ Raw HiFi reads input, in FASTQ format. n/a

Steps

ID Name Description
0 HiFiASM 1o assembly Primary assembly input from hifiasm workflow, in FASTA format.
1 HiFi reads as FASTQ Raw HiFi reads input, in FASTQ format.
2 Step 1. Base-level coverage toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy3
3 Step 1. Run minimap2 to align pacbio data and generate paf files, toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.20+galaxy2
4 Step 1. Split an assembly and do a self-self alignment toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.20+galaxy2
5 Step 1. then calculate read depth histogram and base-level read depth. toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy3
6 Step 2. Purge haplotigs and overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy3
7 Step 3. Get purged primary and haplotig sequences from draft assembly toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy3
8 Haplotype fasta toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.3

Outputs

ID Name Description Type
split_fasta split_fasta n/a fasta
alignment_output alignment_output n/a bam
alignment_output alignment_output n/a bam
stat_file stat_file n/a tabular
pbcstat_cov pbcstat_cov n/a tabular
pbcstat_wig pbcstat_wig n/a wig
hist hist n/a png
calcuts_log calcuts_log n/a txt
calcuts_tab calcuts_tab n/a tabular
purge_dups_log purge_dups_log n/a txt
purge_dups_bed purge_dups_bed n/a bed
get_seqs_hap get_seqs_hap n/a fasta
get_seqs_purged get_seqs_purged n/a fasta
stats stats n/a tabular
help Creators and Submitter
Creator
Submitter
Activity

Views: 95   Downloads: 1

Created: 15th Nov 2021 at 01:39

Last updated: 15th Nov 2021 at 01:40

Last used: 30th Nov 2021 at 03:01

help Attributions

None

Version History

Version 1 Created 15th Nov 2021 at 01:39 by Johan Gustafsson

No revision comments

Related items

Powered by
(v.1.12.0-master)
Copyright © 2008 - 2021 The University of Manchester and HITS gGmbH