CH391L/UTpond
From Marcotte Lab
Contents |
Number of reads
- V3BC21: 213,419 (F3), 199,158 (F5), 223,100 (raw)
- V3BC22: 634,431 (F3), 595,251 (F5), 661,120 (raw)
- V3BC23: 1,015,471 (F3), 951,357 (F5), 1,060,308 (raw)
- V3BC24: 562,803 (F3), 525,892 (F5), 588,304 (raw)
- V3BC25: 569,125 (F3), 531,015 (F5), 595,064 (raw)
You can download CSFASTA files from here.
Databases
- Prokaryotes: http://www.marcottelab.org/users/CH391L/UTpond/NCBI.bacteria/NCBI_bacteria_rep.tgz (835 MB) (870 genomes)
- Source: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/ (2011-Feb-28 version).
- Select one chromosome per species randomly.
- Eukaryotes (Organelle): http://www.marcottelab.org/users/CH391L/UTpond/ENA.organelle/ENA_organelle.fna.gz (2,982 genomes)
Mapping results (SAM file + read_freq)
- Prokaryotes: http://www.marcottelab.org/users/CH391L/UTpond/NCBI.bacteria/
- Eukaryotes: http://www.marcottelab.org/users/CH391L/UTpond/ENA.organelle/
Analysis tool
- SAM : alignment report format
- SHRiMP: Alignment tool http://compbio.cs.toronto.edu/shrimp/
- Never, ever try to run this program on cygnus. It needs lots of memory, so easily kills the computer.
- Paper for original version
- Paper for version 2
$ gsmapper-cs foobar.csfasta db.fasta -E -N 4 -o 1000 -h 80% >foobar.gsmapper_sam 2>foobar.gsmapper_log