lpryszcz/redundans repository overview

Program takes as input assembled contigs, paired-end and/or mate pairs sequencing libraries and returns scaffolded homozygous genome assembly, that should be less fragmented and with total size smaller than the input contigs. In addition, Redundans will automatically close the gaps resulting from genome assembly or scaffolding (more details⁠).

The pipeline consists of three steps/modules:

• redundancy reduction: detection and selectively removal of redundant contigs from an initial de novo assembly
• scaffolding: joining of genome fragments using paired-end and/or mate-pairs reads
• gap closing

Redundans is:

• fast & lightweight, multi-core support and memory-optimised, so it can be run even on then laptop for small-to-medium size genomes
• flexible toward many sequencing technologies (Illumina, 454 or Sanger) and library types (paired-end, mate pairs, fosmids)
• modular: every step can be ommited or replaced by another tools

If you wish to try it, execute:

# process the data inside the image - all data will be lost at the end
docker run -it -w /redundans lpryszcz/redundans ./redundans.py -v -i test/{600,5000}_{1,2}.fq.gz -f test/contigs.fa -o test/run1

# if you wish to process local files, you need to mount the volume with -v
## make sure you are in redundans repo directory (containing test/ directory)
docker run -it -v `pwd`/test:/test:rw lpryszcz/redundans /redundans/redundans.py -v -i test/*.fq.gz -f test/contigs.fa -o test/run1

For more info visit Redundans @ github⁠.