| #creates a base image from condo | |
| FROM continuumio/miniconda3 | |
| SHELL ["/bin/bash", "-c"] | |
| COPY environment.yml . | |
| #run environment | |
| #RUN conda env create -f environment.yml | |
| RUN conda init bash |
| // To compile: | |
| // gcc -g -O2 example.c libminimap2.a -lz | |
| #include <stdlib.h> | |
| #include <assert.h> | |
| #include <stdio.h> | |
| #include <zlib.h> | |
| #include "minimap.h" | |
| #include "kseq.h" | |
| KSEQ_INIT(gzFile, gzread) |
| // a combination of inverse square root (see wiki) and inversion: https://bits.stephan-brumme.com/inverse.html | |
| static inline float mg_sqrtf(float x) | |
| { | |
| union { float f; uint32_t i; } z = { x }; | |
| z.i = 0x5f3759df - (z.i >> 1); | |
| z.f *= (1.5f - (x * 0.5f * z.f * z.f)); | |
| z.i = 0x7EEEEEEE - z.i; | |
| return z.f; | |
| } |
| var getopt = function(args, ostr) { | |
| var oli; // option letter list index | |
| if (typeof(getopt.place) == 'undefined') | |
| getopt.ind = 0, getopt.arg = null, getopt.place = -1; | |
| if (getopt.place == -1) { // update scanning pointer | |
| if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') { | |
| getopt.place = -1; | |
| return null; | |
| } | |
| if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--" |
| ===> Where do you most often perform bioinformatics analysis <=== | |
| 1 Personal computer (laptop/desktop) | |
| 2 Lab server | |
| 3 Departmental server | |
| 4 University server/cluster | |
| 5 Cloud | |
| 6 Other | |
| ===> Type of problems <=== |
| gg:ksw2_ggd.c cli.c ksw2.h | |
| $(CC) -Wall -g -O2 -o $@ ksw2_ggd.c cli.c | |
| clean: | |
| rm -fr *.o *.dSYM gg |
| #include <stdio.h> | |
| #define SIMD_SSE 0x1 | |
| #define SIMD_SSE2 0x2 | |
| #define SIMD_SSE3 0x4 | |
| #define SIMD_SSSE3 0x8 | |
| #define SIMD_SSE4_1 0x10 | |
| #define SIMD_SSE4_2 0x20 | |
| #define SIMD_AVX 0x40 | |
| #define SIMD_AVX2 0x80 |
| Source | Dst. file type | Protocol | Time (s) | Command Line |
|---|---|---|---|---|
| NCBI | .sra | ftp | 296 | wget |
| NCBI | .fastq.gz | sra toolkit | ~23000 | fastq-dump -Z --gzip --split-spot |
| local file | sra=>fastq.gz | sra toolkit | ~15000 | fastq-dump --gzip --split-spot --split-3 |
| EBI | .fastq.gz | aspera | 513+492 | aspera -QT -l 300m |
| EBI | .fastq.gz | ftp | 1876+1946 | wget |
Notes:
| CREATE TABLE seq ( | |
| checksum TEXT, | |
| ac TEXT, -- INSDC sequence accession, when available | |
| len INTEGER, -- could be of type "TEXT"; no need to implement "less than" | |
| seq TEXT, | |
| PRIMARY KEY (checksum) -- what about collisions? | |
| ); | |
| CREATE INDEX seq_len ON seq (len) | |
| CREATE INDEX seq_ac ON seq (ac) -- different checksums may have the same AC |
NA12878 DirectRNA reads were obtained [here][raw-data] (passed reads only) and aligned with [minimap2][minimap2] v2.5 against the no_alt_analysis_set of GRCh38 plus SIRV contigs. It took <1 wall-clock hour across 16 CPU cores with command-line options: -cx splice -k14 --cs -uf -N20 -t16. Alignments were converted to BED with the misc/splice2bed.js script from minimap2 and then converted to BigBed. Ribosome-related genes (RPL*, RPS*, EEF* and RPSA) were excluded to reduce the file size. The final BigBed is hosted [at OSF][osf-prj].
A UCSC custom track is configured with
track type=bigBed name=NA12878-DirectRNA.minimap2-2.5 useScore=1 visibility=4 itemRgb="On" bigDataUrl=https://files.osf.io/v1/resources/b5nm2/providers/osfstorage/5a2347599ad5a10272ed5739?action=download&version=1&direct
You can access this track with the [following link][direct-link]. A GMAP alignment track is temporarily available [here][gmap]. This track contains 1/4 of reads. GMAP is still running. It will take 4–5 wall-clock