Jit
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SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
By BioStar 609 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...MetaSim A Sequencing Simulator for Genomics and Metagenomics.
By Jit 3015 days agoab.inf.uni-tuebingen.de - Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a...
Reverse Complement Problem Solved with Perl
Last updated 3923 days ago by JitQuestion at http://rosalind.info/problems/1b/ #Find the reverse complement of a DNA string.#Given: A DNA string Pattern.#Return: Pattern, the reverse complement of Pattern.use strict;use warnings;my $string="AAAACCCGGT";my $finalString="";my %hash...BioScripts
By Rahul Nayak 3905 days agocode.google.com - You are requested to please bookmark collection of bioinformatics tools, scripts, codes that can be pieced together in a very easy and flexible manner to perform both simple and complex bioinformatics tasks. The next-generation sequencing included...URMAP, an ultra-fast read mapper
By Jit 1954 days ago Comments (1)github.com - URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA with comparable accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calling test with 30× coverage 2×150 reads, URMAP achieves...Comparison of Short Read De Novo Alignment Algorithms
By Rahul Agarwal 4581 days agobiochem218.stanford.edu - Excellent article to introduce different sequencing methods along with tools for de novo assembly of sequencing reads and their relevant references. Title: Comparison of Short Read De Novo Alignment Algorithms Author: Nikhil Gopalcoursera genome assembly tutorial
By Jit 3024 days agogithub.com - Solutions to Coursera Genome Sequencing (Bioinformatics II)COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 3013 days agoftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...3d-dna: 3D de novo assembly (3D DNA) pipeline
By Jit 2991 days agogithub.com - This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017. Unless otherwise...ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
By Seema Singh 2868 days agogithub.com - ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper...
