ONT -- Assembly-Flye-AhrensLab
Version 1

Genome assembly: Flye-based WF for highly repetitive genomes [Schmid et al. NAR 2018]

Inputs

ID Name Description Type
PkorrP19E3_ONT_fast5.tar.gz PkorrP19E3_ONT_fast5.tar.gz n/a n/a
ftp://biftp.informatik.uni-freiburg.de/pub/T0/Ahrens/SRR6982805.fastq ftp://biftp.informatik.uni-freiburg.de/pub/T0/Ahrens/SRR6982805.fastq n/a n/a
external_references external_references runtime parameter for tool filtlong n/a
external_references external_references runtime parameter for tool filtlong n/a
external_references external_references runtime parameter for tool filtlong n/a
input_file input_file runtime parameter for tool filtlong n/a
inputs inputs runtime parameter for tool Assembly n/a
fastq_input fastq_input runtime parameter for tool Map with minimap2 n/a
reference_source reference_source runtime parameter for tool Map with minimap2 n/a
input1 input1 runtime parameter for tool BAM-to-SAM n/a
corrected_reads corrected_reads runtime parameter for tool Racon n/a
overlaps overlaps runtime parameter for tool Racon n/a
reads reads runtime parameter for tool Racon n/a
adv adv runtime parameter for tool Nanopolish variants n/a
adv adv runtime parameter for tool Nanopolish variants n/a
adv adv runtime parameter for tool Nanopolish variants n/a
adv adv runtime parameter for tool Nanopolish variants n/a
adv adv runtime parameter for tool Nanopolish variants n/a
adv adv runtime parameter for tool Nanopolish variants n/a
b b runtime parameter for tool Nanopolish variants n/a
input_merged input_merged runtime parameter for tool Nanopolish variants n/a
input_reads_raw input_reads_raw runtime parameter for tool Nanopolish variants n/a
reference_source reference_source runtime parameter for tool Nanopolish variants n/a

Steps

ID Name Description
0 PkorrP19E3_ONT_fast5.tar.gz
1 ftp://biftp.informatik.uni-freiburg.de/pub/T0/Ahrens/SRR6982805.fastq
2 filtlong toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.0
3 Assembly toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.3.5
4 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.12
5 BAM-to-SAM toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1
6 Racon toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.3.1
7 Nanopolish variants toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_variants/nanopolish_variants/0.1.0

Outputs

ID Name Description Type
outfile outfile n/a fastqsanger
contigs contigs n/a fasta
scaffolds scaffolds n/a fasta
assembly_info assembly_info n/a tabular
assembly_graph assembly_graph n/a graph_dot
flye_log flye_log n/a txt
alignment_output alignment_output n/a bam
output1 output1 n/a sam
consensus consensus n/a fasta
output_polished output_polished n/a fasta
output_variants output_variants n/a vcf
help Creators and Submitter
Creator
  • Milad Miladi
Submitter
License
Activity

Views: 99   Downloads: 9

Created: 5th Aug 2020 at 14:01

Last used: 26th Sep 2020 at 22:57

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