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Installing python-numpy !
Last updated 2960 days ago by Jit$ sudo apt-get install python-numpy python-scipy python-matplotlib ipython ipython-notebook python-pandas python-sympy python-nose[sudo] password for urbe: Reading package lists... DoneBuilding dependency tree Reading state information... DoneThe...
Setting python version as default on Linux
By Rahul Nayak 2839 days agoIf you have a later version than 2.6 you'll need to set 2.6 as the default Python.Nucleus: Python and C++ code for reading and writing genomics data.
By Jit 2323 days agogithub.com - Nucleus is a library of Python and C++ code designed to make it easy to read, write and analyze data in common genomics file formats like SAM and VCF. In addition, Nucleus enables painless integration with the TensorFlow machine learning framework,...snakepipes: A toolkit based on snakemake and python for analysis of NGS data
By Jit 2572 days agogithub.com - snakePipes are flexible and powerful workflows built using snakemake that simplify the analysis of NGS data. DNA-mapping* ChIP-seq* RNA-seq* ATAC-seq* scRNA-seq Hi-C Whole Genome Bisulfite Seq/WGBS (*Also available in...-
Tools for Geospatial data analysis !
Last updated 1180 days ago by BioStarGeospatial data is becoming increasingly important in many fields, including urban planning, environmental science, public health, and more. These tools can help you work with data from a variety of sources, including satellite imagery, GPS data,... -
Run miniasm assembler on nanopore reads !
Last updated 3100 days ago by Jit Comments (5)Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream... -
Frequent Paired-end reads (PE 2x100) mapping command lines
Last updated 2951 days ago by Jitbowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \ && bwa sampe hs37m r1.sai r2.sai r1.fq r2.fq > r12.bwa.sam bwa bwasw... npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
By Shruti Paniwala 2925 days agojapsa.readthedocs.io - npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple...SimLoRD: A read simulator for third generation sequencing reads
By Aaryan Lokwani 2852 days agobitbucket.org - SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model. Reads are simulated from both strands of a provided or randomly generated reference sequence. The reference...
