Linux	Mac OSX

What is Short Read Connector (SRC)?

Short read connector enables the comparisons of two read sets B and Q. For each read from Q it provides either:

• The number of occurrences of each k-mers of the read in the set B (SRC_counter) or
• A list of reads from B that share enough k-mers with the tested read from B (SRC_linker)

Citation Camille Marchet, Antoine Limasset, Lucie Bittner, Pierre Peterlongo. A resource-frugal probabilistic dictionary and applications in (meta)genomics. 2016.

Getting the latest source code

Requirements

CMake 2.6+; see http://www.cmake.org/cmake/resources/software.html

c++ compiler; compilation was tested with gcc and g++ version>=4.5 (Linux) and clang version>=4.1 (Mac OSX).

Instructions

# get a local copy of source code
git clone --recursive https://github.com/GATB/rconnector.git

# compile the code an run a simple test on your computer
cd gatb-rconnector
sh INSTALL

Getting a binary stable release

Binary release for Linux and Mac OSX are provided within the "Releases" tab on Github/rconnector web page.

Quick start

Run a simple test looking for reads from data/c2.fasta.gz that share at least 20 kmers (k=25) with data/c1.fasta.gz. Kmers indexed from data/c1.fasta.gz are those occurring at least 2 times.

 sh short_read_connector.sh -b data/c1.fasta.gz -q data/fof.txt
 
 TODO: explain the FOF concept

Usage

Mimimal call

Calling SRC_linker between read sets bank and query:

sh short_read_connector.sh -b bank -q query

Options

 -p prefix. All out files will start with this prefix. Default="short_read_connector_res"
 -g: with this option, if a file of solid kmer exists with same prefix name and same k value, then it is re-used and not re-computed.
 -k value. Set the length of used kmers. Must fit the compiled value. Default=31
 -f value. Fingerprint size. Size of the key associated to each indexed value, limiting false positives. Default=12
 -G value. gamma value. MPHF expert users parameter - Default=2
 -a: kmer abundance min (kmer from bank seen less than this value are not indexed). Default=2
 -s: minimal number of kmer shared by two reads to be considered as similar. Default=3
 -t: number of thread used. Default=0
 -d: use disk over RAM (slower and no impact with -c option)
 -c: use short_read_connector_counter (SRC_counter)

Output Format

Short reads counter

Command:

 sh short_read_connector.sh -b data/c1.fasta.gz -q data/fof.txt -c

Two first lines of the output file:

 #query_read_id mean median min max number of shared 31mers with banq read set data/c2.fasta.gz
 0 3.614286 4 2 5

The first line is the file header. The second line can be decomposed as:

• 0: id of the query read
• 3.614286: mean number of occurrences of its k-mers (here with k=31) in the read set data/c2.fasta.gz
• 4: median number of occurrences of its k-mers (here with k=31) in the read set data/c2.fasta.gz
• 2: minimal number of occurrences of at least a kmer from read 0 in the read set data/c2.fasta.gz
• 5: maximal number of occurrences of at least a kmer from read 0 in the read set data/c2.fasta.gz

Short reads linker

Command:

 sh short_read_connector.sh -b data/c1.fasta.gz -q data/fof.txt

Two first lines of the output file:

 #query_read_id [target_read_id-kmer_span (k=31)-kmer_span query percentage]* or U (unvalid read, containing not only ACGT characters or low complexity read)
 1:676-93-93.000000 809-89-89.000000

The first line is the file header. The second line can be decomposed as:

• 1: id of the query read
• 676-93-93.000000: a target read and its peaces of information: * 676: id of the targeted read * 93: kmer-span (number of position of read 1 that is covered by at least a solid kmer present in read 676) * 93.000000: ration of kmer-span wrt to read 1 length (here 100)
• 809-89-89.000000: a second targeted read and its peaces of information (and so on)

Input read sets

We use file of files format. The input read sets are provided using a file of file(s). The file of file(s) contains on each line a read file or another file of file(s). Let's look to a few usual cases (italic strings indicate the composition of a file):

• Case1: I've a unique read set composed of a unique read file (reads.fq.gz).

  • fof.txt:
  • reads.fq.gz

• Case2: I've a unique read set composed of a couple of read files (reads_R1.fq.gz and reads_R2.fq.gz). This may be the case in case of pair end sequencing.

  • fof.txt:

    • fof_reads.txt:

    with fof_reads.txt:

    • reads_R1.fq.gz
    • reads_R2.fq.gz

• Case3: I've two read sets each composed of a unique read file: reads1.fq.gz and reads2.fq.gz:

  • fof.txt:
    • reads1.fq.gz
    • reads2.fq.gz

• Case4: I've two read sets each composed two read files: reads1_R1.fq.gz and reads1_R2.fq.gz and reads2_R1.fq.gz and reads2_R2.fq.gz:

  • fof.txt:
    • fof_reads1.txt
    • fof_reads2.txt

  with fof_reads1.txt:

  • reads1_R1.fq.gz
  • reads1_R2.fq.gz

  with fof_reads2.txt:

  • reads2_R1.fq.gz
  • reads2_R2.fq.gz

• and so on...

#Contact

Contact: Pierre Peterlongo: [email protected]