contrib/ guide:

In this directory you will find software developed by various programmers which could be useful to Velvet users:

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- afg_handling by Simon Gladman (Simon.Gladman@csiro.au)

These two scripts allow you to examine the (generally) large .afg files which can be produced by Velvet

	asmbly_splitter allows you to choose a specific scaffold from the assembly and produce a self-standing .afg file for that scaffold.

	snp_view produces an ASCII pileup display of the reads above a given locus

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- VelvetOptimiser by Simon Gladman (Simon.Gladman@csiro.au)

This script automatically finds the optimal parameter settings for Velvet. 

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- estimate-exp_cov by Torsten Seeman (torsten.seemann@infotech.monash.edu.au)

This script automatically determines the expected coverage value as described in the manual, and displays an ASCII histogram, thus obviating the need to start R for each Velvet run.

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- fasta2agp by David Studholme (david.studholme@tsl.ac.uk)

This script converts a Velvet assembly in FastA format with N's in the gaps
into a AGP file which can be submitted to the EMBL or the NCBI.

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- extractContigReads by Daniel Zerbino (zerbino@ebi.ac.uk), suggested by
  Jasper Rees

This script scans the Graph2 file produced by Velvet and produces a FastA file
of all the reads which belong to a given contig. 

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- observed-insert-length by Daniel Zerbino (zerbino@ebi.ac.uk)

This scripts scans the Graph2 file produced by Velvet and computes the insert
length distribution of a chosen short read library in the assembly.

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- shuffleSequences by Eric Cabot (ecabot@wisc.edu) Peter (peter@maubp.freeserve.co.uk) and Daniel Zerbino
  (zerbino@ebi.ac.uk)

Alternative ways to efficiently shuffle your reads produced in the language of
your choice: C, BioPython, Perl or Bash

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- show_repeats by Ken Doig (kdd@doig.org)

Plots out the length of the larger repeated contigs in the assembly. 

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- AssemblyAssembler by Jacob Crawford (jc598@cornell.edu)

Tries out different values of k, then merges all the different assemblies into
one.
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- Columbus Scripts by Daniel Zerbino (dzerbino@soe.ucsc.edu)

Utility scripts used to prepare Columbus reference sequences.

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- select_paired by Konrad Paszkiewicz (K.H.Paszkiewicz@exeter.ac.uk)

Separates paired reads from unpaired read after filtering step

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- MetaVelvet by Yasumbumi Sakakibara et al (yasu@bio.keio.ac.jp)

Modification of Velvet to analyze metagenomic data
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- Pe_read_prepare by Manojkumar Sumathiselvaraju (manojsbiotech@gmail.com)

Preprocessing of paired-end data for de novo genome assembly
