Banana Slug Genomics

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<code> $ sga filter --help Usage: sga filter [OPTION] ... READSFILE Remove reads from a data set. The currently available filters are removing exact-match duplicates and removing reads with low-frequency k-mers. Automatically rebuilds the FM-index without the discarded reads. --help display this help and exit -v, --verbose display verbose output -p, --prefix=PREFIX use PREFIX for the names of the index files (default: prefix of the input file) -o, --outfile=FILE write the qc-passed reads to FILE (default: READSFILE.filter.pass.fa) -t, --threads=NUM use NUM threads to compute the overlaps (default: 1) -d, --sample-rate=N use occurrence array sample rate of N in the FM-index. Higher values use significantly less memory at the cost of higher runtime. This value must be a power of 2 (default: 128) --no-duplicate-check turn off duplicate removal --substring-only when removing duplicates, only remove substring sequences, not full-length matches --no-kmer-check turn off the kmer check --kmer-both-strand mimimum kmer coverage is required for both strand --homopolymer-check check reads for hompolymer run length sequencing errors --low-complexity-check filter out low complexity reads K-mer filter options: -k, --kmer-size=N The length of the kmer to use. (default: 27) -x, --kmer-threshold=N Require at least N kmer coverage for each kmer in a read. (default: 3) Report bugs to js18@sanger.ac.uk </code>

$ qsub -V -cwd -pe mpi 32 initialrun.sh
[jolespin@campusrocks2 SGA]$ cat initialrun.sh.e55293
[timer - sga::filter] wall clock: 23599.21s CPU: 62984.74s
[jolespin@campusrocks2 SGA]$ cat initialrun.sh.o55293
Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.

RLBWT info:
Large Sample rate: 8192
Small Sample rate: 128
Contains 19924474285 symbols in 4702993309 runs (4.2366 symbols per run)
Marker Memory -- Small Markers: 1867919484 (1781.4 MB) Large Markers: 116745024 (111.3 MB)
Total Memory -- Markers: 1984664508 (1892.7 MB) Str: 4702993309 (4485.1 MB) Misc: 152 Total: 6687657969 (6377.847642 MB)
N: 19924474285 Bytes per symbol: 0.335650