Jit
Enthusiast computational biologist with business dream !!!
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SuRankCo: supervised ranking of contigs in de novo assemblies
By Neel 3412 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 3063 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...Rebaler: program for conducting reference-based assemblies using long reads.
By Jit 2930 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 2303 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...RagTag: a collection of software tools for scaffolding and improving modern genome assemblies
By Jit 1841 days agogithub.com - RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include: Homology-based misassembly correction Homology-based assembly scaffolding and patching Scaffold mergingLACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
By Jit 3057 days agoshendurelab.github.io - LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, including source code, documentation and a user's guide are available...Picard
By Neel 3802 days agobroadinstitute.github.io - Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF...Andi
By Jit 3788 days agobioinformatics.oxfordjournals.org - This is the andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient...Bpipe - a tool for running and managing bioinformatics pipelines
By Radha Agarkar 3779 days agohttp://docs.bpipe.org/ - Bpipe provides a platform for running big bioinformatics jobs that consist of a series of processing stages - known as 'pipelines'. January 20th, 2016 - New! Bpipe 0.9.9 released! Download latest, all Documentation Mailing List (Google...
