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[Overview] (#overview)
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[Short Manual] (#manual)
[Eval-AlignGraph] (#eval)
[FAQs] (#faq)
[Erratum] (#error)

2. Installation

   Aligners Bowtie2 and BLAT/PBLAT/NUCMER are required to run AlignGraph.

   • To use Bowtie2 and BLAT/PBLAT/NUCMER, put them to your $PATH: export PATH=PATH2BOWTIE2:$PATH and export PATH=PATH2BLAT/PBLAT/NUCMER:$PATH.
   • The downloaded AlignGraph.cpp file can be compiled with command g++ -o AlignGraph AlignGraph.cpp -lpthread.

3. Inputs

   • Paired-end DNA reads in FASTA format.
   • De novo contigs or scaffolds assembled by any de novo DNA-Seq assembler (Velvet, ABySS, ALLPATHS-LG, SOAPdenovo, etc.).
   • Reference genome from a closely related species.

4. Using AlignGraph

   AlignGraph --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa --genome genome.fa --distanceLow distanceLow --distanceHigh distancehigh --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa [--kMer k --insertVariation insertVariation --coverage coverage --part p --fastMap --ratioCheck --iterativeMap --misassemblyRemoval --resume]
   

   Inputs:
   --read1 is the the first pair of PE DNA reads in fasta format.
   --read2 is the the second pair of PE DNA reads in fasta format.
   --contig is the initial contigs/scaffolds in fasta format.
   --genome is the reference genome in fasta format.
   --distanceLow is the lower bound of alignment distance between the first and second pairs of PE DNA reads (recommended: max{insert length - 1000, single read length}).
   --distanceHigh is the upper bound of alignment distance between the first and second pairs of PE DNA reads (recommended: insert length + 1000).
   Outputs:
   --extendedContig is the extended contig/scaffold file in fasta format.
   --remainingContig is the not extended initial contig/scaffold file in fasta format.
   Options:
   --kMer is the k-mer size (default: 5).
   --insertVariation is the standard variation of insert length (default: 100).
   --coverage is the minimum coverage to keep a path in de Bruijn graph (default: 20).
   --part is the number of parts a chromosome is divided into when it is loaded to reduce memory requirement (default: 1).
   --fastMap calls NUCMER to make fast but less sensitive and accurate contig alignment instead of BLAT (default: none).
   --ratioCheck checks read alignment ratio to the reference beforehand and warns if the ratio is too low; may take a little more time (default: none).
   --iterativeMap aligns reads to one chromosome and then another rather than directly to the genome, which increases sensitivity while loses precision (default: none).
   --misassemblyRemoval detects and then breaks at or removes misassembed regions (default: none).
   --resume resumes the previous unfinished running from several checkpoints (default: none).

5. Outputs

   • Extended contigs or scaffolds in FASTA format. The format of the specification for each extended contig or scaffold (the string following the '>' of FASTA file) is: AlignGraphX @ chromosomeID : contig/scaffoldID ; contig/scaffoldID ; contig/scaffoldID ... : partY, where chromosomeID is the specification of the reference chromosome used to generate the extended contig or scaffold, X is a number starting from 0 to identify the extended contig or scaffold for each reference chromosome, and contig/scaffoldIDs are the specifications of the extendable contigs or scaffolds. If misassemblyRemoval is specified, partY shows the Y-th subcontig or subscaffold of the misassembled contig or scaffold split at misassemblies.
   • Remaining contigs or scaffolds not extended in FASTA format.

6. Example commandline

   Given PE reads files reads_1.fa and reads_2.fa with single read length 100 bp and insert length 500 bp, --distanceLow could be max{500 - 1000, 100} = 100 and --distanceHigh could be 500 + 1000 = 1500, so the simplest commandline with pre-assembled contigs file contigs.fa and reference genome genome.fa should be:

AlignGraph --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa --genome genome.fa --distanceLow 100 --distanceHigh 1500 --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa