Jit
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DAGchainer: Computing Chains of Syntenic Genes in Complete Genomes
By Abhimanyu Singh 2817 days agodagchainer.sourceforge.net - The DAGchainer software computes chains of syntenic genes found within complete genome sequences. As input, DAGchainer accepts a list of gene pairs with sequence homology along with their genome coordinates. Using a scoring function which accounts...ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data
By Jit 2810 days agogithub.com - ConPADE (Contig Ploidy and Allele Dosage Estimation), a probabilistic method that estimates the ploidy of any given contig/scaffold based on its allele proportions. In the process, they report findings regarding errors in sequencing. The method can...PBSuite: Software for Long-Read Sequencing Data from PacBio
By Jit 2807 days agosourceforge.net - PBJelly - the genome upgrading tool. PBHoney - the structural variation discovery tool Both are contained within the PBSuite code found in downloads.----- PBJelly -----Read The...bpRNA: large-scale automated annotation and analysis of RNA secondary structure
By Rahul Nayak 2357 days agogithub.com - bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with...MyCC: Accurate binning of metagenomic contigs via automated clustering sequences using information...
By Jit 2803 days agosourceforge.net - MyCC, an automated binning tool that combines genomic signatures, marker genes and optional contig coverages within one or multiple samples, in order to visualize the metagenomes and to identify the reconstructed genomic fragments. More...SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
By BioStar 1540 days agogithub.com - SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes...Prokka: tool for the rapid annotation of prokaryotic genomes
By Jit 2800 days agowww.vicbioinformatics.com - Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. It produces GFF3, GBK and SQN files...SeqMule: Automated human exome/genome variants detection
By BioStar 1721 days agodoc-openbio.readthedocs.io - SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its...COCACOLA (binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and...
By Jit 2799 days agogithub.com - COCACOLA is a general framework that combines different types of information: sequence COmposition, CoverAge across multiple samples, CO-alignment to reference genomes and paired-end reads LinkAge to automatically bin contigs into OTUs. Furthermore,...Python vs Perl
Started by Rahul Agarwal 4134 days ago Replies (6) Last reply by Jit 2364 days agoWhy bioinformatician still using Perl when Python is easy to code, good in ReXp and faster than perl?
