Jit
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HASLR: a hybrid assembler which uses both second and third generation sequencing reads
By BioStar 1712 days agogithub.com - HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1050 days agogithub.com - This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...SuRankCo: supervised ranking of contigs in de novo assemblies
By Neel 2788 days agosourceforge.net - SuRankCo is a machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which...Metassembler: merging and optimizing de novo genome assemblies
By Rahul Nayak 2439 days agosourceforge.net - Metassembler combines multiple whole genome de novo assemblies into a combined consensus assembly using the best segments of the individual assemblies. Genome assembly projects typically run multiple algorithms in an attempt to find the single best...SALSA: A tool to scaffold long read assemblies with Hi-C
By Jit 2401 days agogithub.com - This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version,...Rebaler: program for conducting reference-based assemblies using long reads.
By Jit 2306 days agogithub.com - Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences. I made Rebaler for bacterial genomes (specifically for the...Merqury: reference-free quality and phasing assessment for genome assemblies
By Jit 1679 days agogithub.com - Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality...Minipolish: A tool for Racon polishing of miniasm assemblies
By BioStar 1865 days agogithub.com - Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not include a polishing step, so its assemblies have a high error rate – they are essentially made of stitched-together pieces of long...merqury: Evaluate genome assemblies with k-mers
By Jit 1652 days agogithub.com - Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality...Syri compares alignments between two chromosome-level assemblies and identifies synteny and...
By Shruti Paniwala 954 days agogithub.com - Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.
