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"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
author galaxy-australia
date Wed, 08 Feb 2023 04:31:08 +0000
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1 *A Galaxy Wrapper of IPA HiFi Genome Assembler*
2
3 **Description**
4
5 This repo contains the implementation of the IPA HiFi Genome Assembler. It's currently implemented as a Snakemake workflow (workflow/ipa.snakefile) and runs the following stages:
6
7 1. Building the SeqDB and SeedDB from the input reads.
8 2. Overlapping using the Pancake overlapper.
9 3. Phasing the overlaps using the Nighthawk phasing tool.
10 4. Filtering the overlaps using Falconc m4Filt.
11 5. Contig construction using Falcon's ovlp_to_graph and graph_to_contig tools.
12 6. Read tracking for read-to-contig assignment.
13 7. Polishing using Racon.
14
15 For more info: https://github.com/PacificBiosciences/pbipa and https://github.com/PacificBiosciences/pbbioconda/wiki/Improved-Phased-Assembler
16
17 *test-data*
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19
20 The test data can be downloaded from ([bam](https://downloads.pacbcloud.com/public/dataset/2021-11-Microbial-96plex/demultiplexed-reads/m64004_210929_143746.bc2046.bam)) or select one of the bam files [here](https://downloads.pacbcloud.com/public/dataset/2021-11-Microbial-96plex/demultiplexed-reads/) or a small ccs bam (85MB) bam file [here](https://downloads.pacbcloud.com/public/dataset/ISMB_workshop/isoseq3/alz.ccs.bam)
21
22 *planemo test*
23
24 1. download the m64004_210929_143746.bc2046.bam file into test-data folder
25 2. create a softlink (test.bam) pointing to m64004_210929_143746.bc2046.bam
26
27 3. run planemo test (i.e. planemo test --galaxy_root=/path/to/your/galaxy/folder ipa.xml)
28 or
29 3. run planemo test --update_test_data (i.e. planemo test --galaxy_root=/path/to/your/galaxy/folder ipa.xml) to update the test data
30 or
31 3. run planemoe test (i.e. planemo test --galaxy_root=/path/to/your/galaxy/folder ipa.xml)
32