Results for "De Bruijn graph"

Bio-Scripts

  • Estimate Genome Size

    # Count k-mer occurrence using Jellyfish 2.2.6 jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? sread_1.fastq sread_2.fastq # points for a histogram jellyfish histo -o 19mer_out.histo 19mer_out #Plot results using R ##load the data into dataframe19 dataframe19

    2227 days ago

  • Estimate Genome Size with Jellyfish and R

    jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? /common/Tutorial/Genome_estimation/sample_read_1.fastq /common/Tutorial/Genome_estimation/sample_rea...

    2208 days ago

  • Running Trinity on RNA-seq !

    ...----- Chrysalis ------------------------- -- (Contig Clustering & de Bruijn Graph Construction) -- -----------...Running CMD: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/Chrysalis/GraphFromFasta -i /home/urbe/Tools/...

    2090 days ago

  • Installing ggplot2 and its dependencies on Ubuntu !

    jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter/minidot/bin$ sudo R [sudo] passw...rror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/graph.c -o utf8lite/src/graph.o gcc -std=gnu99 -I/usr/shar...

    1512 days ago

  • Pack a perl program with their dependencies on Ubuntu !

    #Follow steps to create your own executable ./web jit@j...uenceTubeMapsdisplaysmultiplegenomicsequencestubemapgraphmap github.com - A Jav...pt module for the visualization of genomic sequence graphs. It automatically generates...

    1474 days ago

  • Setting up autoConTAMPR !

    (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 --...

    1404 days ago

  • Install prokka using conda !

    (JitMetaENV) ➜ assembly conda install -c bioconda prokka Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen s...

    1178 days ago

  • Install Bwise using conda !

    ...: done Verifying transaction: done Executing transaction: done (JitMetaENV) ➜ test_phase_assebly bwise *** This is BWISE - High order De Bruijn graph assembler *** The command...

    952 days ago

  • Tadpole is 250x faster than SPADes assembler !

    lege@jit-Lenovo-ideapad-320-15ISK:~/Downloads/MyTools/Vir$...flags. dot= Write a contigs connectivity graph (partially implemented) dump...processcontigs=f Explore the contig connectivity graph. (partially implemented) P...

    938 days ago

  • Install mgsc on Ubuntu !

    (abhiENV) [abhi@hn1 output_OM824]$ c...added / updated specs: - graphviz - numpy - python...4ff587b_1 1.7 MB graphviz-2.40.1 |...64::glib-2.69.1-h4ff587b_1 graphite2 pkgs/main/linux-...#################### | 100% graphviz-2.40.1 | 6.5 MB |...

    787 days ago