Results for "Computational Tools"
Bio-Scripts
➜ Tools git:(master) ✗ wget https://github.com/samtools/htslib/releases/download/1.9/...saved [1178859/1178859] ➜ Tools git:(master) ✗ tar -vxjf htsl....in htslib-1.9/configure ➜ Tools git:(master) ✗ cd htslib-1.9...-I. -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c gc...2020 days ago
Installing Platypus on Ubuntu !
...l -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -...o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/file...ter release! File: /home/urbe/Tools/Platypus/src/cython/fastafile...ter release! File: /home/urbe/Tools/Platypus/src/cython/cwindow.p...2020 days ago
Setting up falconUnzip conda environments for genome assembly !
...83 KB conda-forge setuptools-40.6.2 | p...bioconda bcftools: 1.9-h4da6232_...conda-forge samtools: 1.9-h8ee4bcc_...# # PacBio(R) tools distributed via Bioconda are:...1990 days ago
- Download page https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYP...1+-x64-linux.tar.gz # add BLAST location to system PATH export PATH=$HOME/tools/BLAST/ncbi-blast-2.8.1+/bin:$...
1762 days ago
Perl script to run in parellel !
#!/usr/bin/perl use strict; use warnings; use Parallel::ForkManager; use Bio::SeqIO;...--species=caenorhabditis --outfile=$fn $seq --AUGUSTUS_CONFIG_PATH=/home/urbe/Tools/Alienomics_v1.1/augustus.2.5....1687 days ago
Bash script to download SRA file !
#We can use the sratoolkit to directly pull the sequence data (in paired FASTQ format) from...r compressed format (SRA!) that isn't directly compatible with any downstream tools, so it's necessary to put thi...1560 days ago
Commands to install conda in Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads$ mkdir jittmp...right to change w hich third party tools are provided in Anaconda Dist...he904b0f_5 ... installing: more-itertools-6.0.0-py37_0 ... installing:...e-0.5.7-py37_1 ... installing: setuptools-40.8.0-py37_0 ... installing...1512 days ago
- (base) jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ docker build -t autocontampr . Sending build context to Docker daemon 9.024MB Step 1/16 : FROM ubuntu:14.04 --...
1443 days ago
picard tools command to get some insert statistics
#picard tools to get some insert statistics to see whether our reads seem to be in the correct place #module load picard/2.0.1 java -Xmx16g -XX:PermSize=8g -jar $PICAR...1337 days ago
- (JitMetaENV) ➜ assembly conda install -c bioconda prokka Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen s...
1216 days ago
