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Innocenture project

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Modified on 2013/03/22 21:32 by Ben Fulton Categorized as Uncategorized
Sequencing bias? Pacbio tends to error by insertions or deletions. Can we figure out what the error profile is of the Pacbio sequencing?

Information from supercomputer filesystem

:/N/dc/scratch/yye/InnoCentive/Software> cat README

>> Samtools SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

>> Reads mapping tools Bowtie BWA

>> Assembly tools Velvet Newbler (not installed)

>>BLAST

yes, the famous BLAST



befulton@BigRed:/N/dc/scratch/yye/InnoCentive/Software> ls
  • bowtie2-2.0.0-beta4
  • bwa-0.6.2
  • README
  • bowtie2-2.1.0
  • ncbi-blast-2.2.26+
  • samtools-0.1.18



befulton@BigRed:/N/dc/scratch/yye/InnoCentive/Software>

FN - index file for human genome

befulton@BigRed:/N/dc/scratch/yye/InnoCentive/Database> ls db download.py human nt.tar befulton@BigRed:/N/dc/scratch/yye/InnoCentive/Database> ls human command.sh hs37.fa.nhr hs37.srprism.amp hs37.srprism.map hs37.srprism.ss hs37.bitmask hs37.fa.nin hs37.srprism.idx hs37.srprism.pmp hs37.srprism.ssa hs37.fa hs37.fa.nsq hs37.srprism.imp hs37.srprism.rmp hs37.srprism.ssd

befulton@BigRed:/N/dc/scratch/yye/InnoCentive/Database> cat human/command.sh
  1. !/bin/sh
    bmtool -d hs37.fa -o hs37.bitmask -w 18
    srprism mkindex -i hs37.fa -o hs37.srprism -M 7168
    makeblastdb -in hs37.fa -dbtype nucl

Also MEGAN http://en.wikipedia.org/wiki/MEGAN

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