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Tasks #1

Open

24 of 30 tasks

sjackman opened this issue Oct 18, 2019 · 0 comments

Open

24 of 30 tasks

Tasks #1

sjackman opened this issue Oct 18, 2019 · 0 comments

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sjackman commented Oct 18, 2019 •

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Assemble the linked reads (LR) with non-LR-aware assemblers
- @bernieyiweizhao Unicycler
- @haghshenas SPAdes
- @haghshenas ABySS
Scaffold these assemblies using ARCS
- @bernieyiweizhao Unicycler
- @haghshenas SPAdes
- @haghshenas ABySS
Assemble the linked reads (LR) with LR-aware assemblers
- @gapalm ABySS
- @emreerhan cloudSPAdes
- @gapalm Supernova
@schutzekatze @thezange @trgibbons Devise a system to index a BGZIP (block gzip) compressed FASTQ file of linked reads and efficiently extract the reads from a specified set of barcodes
- Research off-the-shelf tools for this purpose
@schutzekatze Identify and extract subsets of barcodes, each derived from one shotgun assembly contig
@afshinfard Identify and extract subsets of barcodes, each subset from overlapping regions of ~100–200 kbp
Assemble these regions using non-LR-aware assemblers
- ABySS
- @thezange Meraculous
- @haghshenas @sjackman SPAdes
- @sjackman Unicycler
Merge these targeted sub-assemblies using a long-read assembler
- Canu
- @haghshenas @sjackman Miniasm
- @sjackman Unicycler
- @thezange wtdbg2 (Redbean)
@schutzekatze Create a setup.py file
🍻
🍻🍻
🍻🍻🍻

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