Open sjackman opened 5 years ago
I worked on updating contigvalidator to use snakemake, getting it to install smoothly, and getting it into a bioconda package. The first part is done
Created a Unicycler component with QUAST for assessment for the text-based workflow system Snakemake. The workflow system produces bacterial genome assemblies from short sequencing reads using Unicycler and evaluates the assembly using QUAST.
I created Flowcraft components for QUAST and Bandage. I used Flowcraft to assemble the Shigella sonnei short reads using SPAdes, assess the assembly quality using QUAST, and visualize the assembly graph using Bandage. See https://github.com/hackseq/modular-assembly-hs18/tree/master/flowcraft/spades and https://github.com/assemblerflow/flowcraft/pull/147 and https://github.com/assemblerflow/flowcraft/pull/150
I worked on a hybrid assembly using ABySS and LINKS for three Shigella sonnei plasmids. Assembled short reads with ABySS (k=96). Scaffolded the contigs with LINKS, using long reads.
The list of what I did:
Initially the https://github.com/GFA-spec/assembler-components repository had specifications for some assembly components, and 2 scripts that showed how the ABySS and bcalm assemblers could be combined.
During the hackathon I modularized those scripts into 5 components:
and used these components to build 3 pipelines:
They've been uploaded to https://github.com/GFA-spec/assembler-components Corresponding Singella assemblies were created and visualized using Bandage.
Create bcalm bioconda and flowcraft recipes.
Run long-read only assembly.
I worked on creating a flowcraft component for Unicycler, but got into too many errors, and couldn't manage to debug everything on time! For reference of picking up on it for future Frankenstein assemblers here is my commit: https://github.com/figalit/flowcraft/commit/e554d87dc75d19b1aa635752f26b84059ee45e31 . I also helped our Reva with R, and joining together all the data for displaying the leaderboard. I also added the project abstract and initial slides for the group.
Bioconda
bcalm
recipe for Bioconda @natirFlowcraft
abyss
component @emreerhan https://github.com/assemblerflow/flowcraft/pull/146bcalm
component @natir https://github.com/assemblerflow/flowcraft/pull/149kmergenie
component @paaksumunicycler
component @sjackman https://github.com/assemblerflow/flowcraft/pull/156quast
component @sjackman https://github.com/assemblerflow/flowcraft/pull/147bandage
component @sjackman https://github.com/assemblerflow/flowcraft/pull/150Snakemake
unicycler
component @pkong97Shell
Leader Board