MADAM - iMproving Ancient Dna AsseMbly

Dependencies

The following software has to be installed in order for the software to run:

• jdk7+
• bwa: http://bio-bwa.sourceforge.net/
• samtools: http://samtools.sourceforge.net/
• ClipAndMerge: https://github.com/apeltzer/ClipAndMerge
• sga: https://github.com/jts/sga
• SOAPdenovo2: https://sourceforge.net/projects/soapdenovo2/files/SOAPdenovo2/
• MEGAHIT: https://github.com/voutcn/megahit
• qualimap: http://qualimap.bioinfo.cipf.es/

Note: Clip&Merge is actually a java program. For correct usage, the program has to be wrapped in a starter script that can be set in the MADAM script.This starter script should contain the following line:

java -jar ClipAndMerge $*

generating the jar file

This program can be built with gradle (https://gradle.org). for that just type

gradle build

The jar-files are then contained in the build/libs folder

Tools

The following tools are available:

assembly

perform an assembly on input data

Parameters:

• SOAP: Run the assembly using SOAPdenovo2
  • -i, --input : the input File(s)
  • -k, --kmer : the Kmers to use
  • -o, --output : the output Directory
  • -p, --prefix : the prefix for the output files [genome]
  • -s, --insertSize : the insert size of the input[20]
  • -t, --threads : number of threads to use [1]
• MEGAHIT: Run the assembly using MEGAHIT
  • -i, --input : the input File(s)
  • -k, --kmer : the Kmers to use
  • -o, --output : the output Directory
  • -t, --threads : number of threads to use [1]

cm

run Clip And Merge on FastQ Files

Parameters:

• -f, --forward : the forward adapter [AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC]
• -h, --help: show this help page
• -in1, --input1 : Forward reads input file(s) in fastq(.gz) file format
• -in2, --input2 : Reverse reads input file(s) in fastq(.gz) file format
• -l, --log : File for Log output [stdout]
• -n, --nomerge: don't merge, just clip and trim
• -o, --output : the output Directory
• -q, --quality : Minimum base quality for quality trimming [20]
• -r, --reverse : the reverse adapter [AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA]
• -s, --single: don't merge and combine for single end assembly (implies -n)

filter

Filter contigs based on length and/or read concurrency

Parameters:

• -f, --filter : the name of the filtered contigs [contigs_filtered.fasta]
• -h, --help: show this help page
• -i, --input : the input contig File to filter
• -l, --length : the minimum length of a contig to keep [NULL]
• -m, --minFilter : the minimum number of reads that have to map against a contig to keep [1]
• -o, --output : the output Directory
• -p, --prefix : the prefix for the mapping files [mapped]
• -q, --fastq : the input fastQ File(s) to filter
• -t, --threads : number of threads to use [1]

Note: Keep in mind that either -l or -q has to be given

merge

Merge different Contig Files into one file using SGA

Parameters:

• -f, --file : name of the merged output file [merged.fasta]
• -h, --help: show this help page
• -i, --input : the input File(s)
• -o, --output : the output Directory
• -t, --threads : number of threads to use [1]

pipeline

Run the pipeline as described in the paper "Improving ancient DNA genome assembly"

Parameters:

• -a, --assembly : The assembly algorithm of the first Layer: SOAP, MEGAHIT [SOAP]
• -f, --forward : the forward adapter [AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC]
• -h, --help: show this help page
• -in1, --input1 : the forward and reverse fastq files
• -in2, --input2 : the forward and reverse fastq files
• -k, --kmer : the Kmers to use [37,47,...,127]
• -l, --filterlength : the minimum length of a contig to keep [1000]
• -m, --minFilter : the minimum number of reads that have to map against a contig to keep [1]
• -n, --no_merge: Do not merge the reads
• -o, --output : the output Directory
• -q, --quality : Minimum base quality for quality trimming [20]
• -r, --reverse : the reverse adapter [AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA]
• -R, --reference : the reference genome file
• -s, --insertSize : the insert size of the input[20]
• -S, --single: don't merge and combine for single end assembly (implies -n)
• -t, --threads : number of threads to use [1]

statistics

Calculate statistical values on contig files

Parameters:

• -h,--help: show this help page
• -i,--input : the list of input Files
• -l,--length : length of reference
• -n,--names : The names of the samples
• -o,--output : the output file [stdout]
• -t,--threads : number of threads to use [1]

mapping

Map the contigs against a reference, run qualimap on the mapping and extract the contigs that could be mapped against the reference

Parameters:

• -h,--help: show this help page
• -i,--input : the input contig File to filter
• -o,--output : the output Directory
• -p,--prefix : the prefix of the bam file [mapped]
• -R,--reference : the reference genome file
• -t,--threads : number of threads to use [1]

wget https://archive.org/download/github.com-Integrative-Transcriptomics-MADAM_-_2018-08-06_06-06-30/Integrative-Transcriptomics-MADAM_-_2018-08-06_06-06-30.bundle

 git clone Integrative-Transcriptomics-MADAM_-_2018-08-06_06-06-30.bundle 

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