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bcgsc / LongStitch

Correct and scaffold assemblies using long reads
GNU General Public License v3.0
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output filenames? #61

Closed margaretc-ho closed 1 year ago

margaretc-ho commented 1 year ago

I am trying to decipher the files that are output from longstitch image

If this was my command: longstitch \ tigmint-ntLink-arks \ k_ntLink=$40 \ w=500 \ gap_fill=True \ draft=tc.contigs \ reads=Tc_combined_run_all_pass.minION.atleast10kb \ G=60000000 \ Which filename includes the final longstitched contigs with gap fills? I am also confused because the filenames are sorted from most recent to older (based on timestamp created).

Thanks in advance!

lcoombe commented 1 year ago

Hi @margaretc-ho,

If you take a look in the log messages from the LongStitch, there should be a final message that tells you which the final file is. The image above it cut off a bit, but the final scaffolds in this case are in the file with the suffix .tigmint-ntLink-arks.longstitch-scaffolds.fa. It's a soft-link to the file with a longer file name (containing the final scaffolds).

Thanks for your interest in LongStitch! Lauren

margaretc-ho commented 1 year ago

Thank you! I was able to confirm the right file in the log files, and double check that they do not have gaps (using fasta_stats)