INTRO

We received PacBio data back from Angie Shmoldt at the Univ. of Wisconsin-Milwaukee as part of Rick’s Salvelinus namaycush sequencing project.

Data was downloaded and MD5 checksums were verified.

Note

Data was downloaded via sftp using the program lftp, as it was the only way I could figure out how to recursively download the data via command line (SSH access was not an option). Here’s the example:

lftp sftp://user@hostname
lftp> mirror /remote/directory /local/destination/

Data is available here:

https://owl.fish.washington.edu/nightingales/S_namaycush/LakeTrout/

Data

Barcoding information can be found in this Excel file:

https://owl.fish.washington.edu/nightingales/S_namaycush/LakeTrout/SampleBarcodes_Goetz.xlsx

Table 1: Pool 1 Barcodes

Pool 1	Sample	Adapter barcode
Lean	FA047	bc2041 TATGATCACTGAGTAT
Siscowet	FA097	bc2071 CGAGTCTAGCGAGTAT
Siscowet	FA099	bc2072 TATCAGTAGTGAGTAT

Table 2: Pool 2 Barcodes

Pool2	Sample	Adapter barcode
Lean	FA094	bc2069 TCTATGACATGAGTAT
Lean	FA095	bc2070 TACTGCTCACGAGTAT
Siscowet	FA100	bc2073 ATCACTAGTCGAGTAT

There are two “pools” of data, which exist as BAM files:

Pool 1
- BAM
  - https://owl.fish.washington.edu/nightingales/S_namaycush/LakeTrout/Pool1/hifi_reads$ md5sum m84082_250614_081210_s3.hifi_reads.bam (22GB)
  - MD5: 58f6d02a4a8e4a96a9c67cead15f2363
- Report (PDF)
  - https://owl.fish.washington.edu/nightingales/S_namaycush/LakeTrout/Pool1/statistics/m84082_250614_081210_s3.report.pdf
Pool 2
- BAM
  - https://owl.fish.washington.edu/nightingales/S_namaycush/LakeTrout/Pool2/hifi_reads/m84082_250614_101514_s4.hifi_reads.bam (19GB)
  - MD5: a406ece54be24ca78257109a57c367a8
- Report (PDF)
  - https://owl.fish.washington.edu/nightingales/S_namaycush/LakeTrout/Pool2/statistics/m84082_250614_101514_s4.report.pdf

Checksum verification

No MD5 checksums were provided, however, the files were hosted on a Synology server, so I was able to generate checksums using the web interface. I manually compared those with the checksums I generated for the files once they were on Owl.