Abhimanyu Singh
A bioinformatics beginner
Our Sponsors
Related items
MeGAMerge: A tool to merge assembled contigs, long reads from metagenomic sequencing runs
By Jit 2897 days agogithub.com - MeGAMerge MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing runs) Description MeGAMerge is a perl based wrapper/tool that can accept any number of sequence (FASTA) files containing assembled contigs of any...splitbam: splits a BAM by chromosomes
By Jit 2826 days agocode.google.com - splitbam splits a BAM by chromosomes. Using the reference sequence dictionary (*.dict), it also creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to...Long read assembly workshop !
By Rahul Nayak 2242 days ago Comments (4)sepsis-omics.github.io - This is a tutorial for a workshop on long-read (PacBio) genome assembly. It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and...VCF Compare !
By Rahul Nayak 1040 days agowiki.bits.vib.be - compare two BWA mapping methods with the online hg18-mapped data We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep...CoLoRMap: Correcting Long Reads by Mapping short reads
By Jit 2287 days agogithub.com - Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies....Ensembl comparative genomics resources
By Jitendra Narayan 3191 days agowww.ncbi.nlm.nih.gov - The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny,...BUSCO
By Jitendra Narayan 3212 days agohttp://busco.ezlab.org/ - Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs More at http://busco.ezlab.org/CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.
By Jit 3134 days ago Comments (2)github.com - Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered. Canu is...YASS :: genomic similarity search tool
By Jit 3128 days agobioinfo.lifl.fr - YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments). Like most of the heuristic pairwise local alignment tools for DNA sequences (FASTA, BLAST,...MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping
By Neel 3109 days agojournals.plos.org - MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies,...
