Comments (2)
lcoombe
commented on June 6, 2024
Hello @Grelot
The BAM files are alignments of the linked reads to the draft scaffolds. We use bwa mem to generate these files.
Take a look at our Makefile (Examples/arcs-make), which you can directly use to run the entire ARCS pipeline, or at least will give you some guidance about the steps (and parameters/options) required in the pipeline.
Hope that helps!
Lauren
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lcoombe
commented on June 6, 2024
@Grelot - I'll close this, but feel free to re-open/open another issue if you have any further questions!
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Related Issues (20)
- Regarding the error info "File contains unpaired reads" HOT 7
- About Running ARCS in default mode HOT 3
- GCC version update HOT 1
- arcs-1.2.2: abyss-fixmate-ssq sometimes segfaults HOT 9
- Short read length question: can the tool accept 250? HOT 2
- arcs-long: tiny PE-pairs are produced HOT 3
- Scaffolding Expectations HOT 12
- Running ARCS and ARKS HOT 2
- Parameters for corrected ONT reads HOT 2
- arcs-make in bin HOT 2
- Add optional dependency of pigz HOT 1
- unrecognized option '--fastq' HOT 3
- fastq formatting barcodes in BX tag HOT 8
- ARKS fails to create any links with a highly repetitive input HOT 4
- Parameters for PacBio HiFi data HOT 3
- Can this software use HiC data, or need to use the sequencing technology mentioned in your paper? HOT 1
- `arcs-tigmint` and `arks-tigmint` struggle with input files outside working directory HOT 3
- Incorrect program call? HOT 6
- `arcs-long`/`arks-long` vs `LINKS`? HOT 2
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