Tasks

[sjackman]

Bioconda

• Create a bcalm recipe for Bioconda @natir

Flowcraft

• Create an abyss component @emreerhan Added an abyss component to flowcraft, and added a new disableRR parameter to spades assemblerflow/flowcraft#146
• Create a bcalm component @natir Add bcalm flowcraft assemblerflow/flowcraft#149
• Create a kmergenie component @paaksum
• Create a unicycler component @sjackman Add unicycler assemblerflow/flowcraft#156
• Create a quast component @sjackman Add quast assemblerflow/flowcraft#147
• Create a bandage component @sjackman Add bandage assemblerflow/flowcraft#150

Snakemake

• Create a unicycler component @pkong97
• Validate contigs @pashadag
• Hybrid assembly using ABySS + LINKS @sm30

Shell

• Create independent abyss and bcalm components as shell scripts @rchikhi
• Demonstrate a small pipeline with the above scripts @rchikhi
• Added gfaview as a component @rchikhi
• Make more shell components in the spirit of those done in https://github.com/GFA-spec/assembler-components

Leader Board

• Create the Awesome Assemblies leader board using Shiny @figalit @scatcher125

[pashadag]

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

[pkong97]

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.

[sjackman]

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 assemblerflow/flowcraft#147
and assemblerflow/flowcraft#150

[sm30]

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.

[emreerhan]

The list of what I did:

• I created a FlowCraft component for ABySS!
• I added an option to disable repeat resolution in the SPAdes FlowCraft component
• I generated bandage plots and quast statistics for ABySS using FlowCraft
• I also created the franken-assembler SPAdes-ABySS (or SPABySS), where SPAdes is run without error correction or repeat resolution, and the unitigs are sent to ABySS for processing all the way to scaffolds.

[rchikhi]

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:

• abyss_contigs_from_unitigs.sh
• abyss_scaffolding.sh
• abyss_unitigs.sh
• bcalm.sh
• gfaview_contigs_from_unitigs.sh

and used these components to build 3 pipelines:

• ABySS
• BCALM then ABySS
• BCALM then gfaview then ABySS

They've been uploaded to https://github.com/GFA-spec/assembler-components
Corresponding Singella assemblies were created and visualized using Bandage.

[natir]

Create bcalm bioconda and flowcraft recipes.

Run long-read only assembly.

[figalit]

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: figalit/flowcraft@e554d87 .
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.