Mercurial > repos > galaxy-australia > ipa_hifi

annotate README.md @ 0:f78303e25f3e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
parents
children 1289beb50ab0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
1 *A Galaxy Wrapper of IPA HiFi Genome Assembler*
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
2
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
3 **Description**
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
4
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
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:
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
6
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
7 1. Building the SeqDB and SeedDB from the input reads.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
8 2. Overlapping using the Pancake overlapper.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
9 3. Phasing the overlaps using the Nighthawk phasing tool.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
10 4. Filtering the overlaps using Falconc m4Filt.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
11 5. Contig construction using Falcon's ovlp_to_graph and graph_to_contig tools.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
12 6. Read tracking for read-to-contig assignment.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
13 7. Polishing using Racon.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
14
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
15 For more info: https://github.com/PacificBiosciences/pbipa and https://github.com/PacificBiosciences/pbbioconda/wiki/Improved-Phased-Assembler
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
16
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
17 *test-data*
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
18
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
19
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
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)
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
21
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
22 *planemo test*
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
23
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
24 1. download the m64004_210929_143746.bc2046.bam file into test-data folder
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
25 2. create a softlink (test.bam) pointing to m64004_210929_143746.bc2046.bam
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
26
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
27 3. run planemo test (i.e. planemo test --galaxy_root=/path/to/your/galaxy/folder ipa.xml)
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
28 or
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
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
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
30 or
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
31 3. run planemoe test (i.e. planemo test --galaxy_root=/path/to/your/galaxy/folder ipa.xml)
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
32