Genome assembly stats plotting
...ngth Number of scaffolds/contigs Length of longest scaffold/contig Scaffold/contig N50 and N90Assembly base composition, in particular percentage GC and percentage Ns CEGMA comp...2257 days ago
An Introduction to Applied Bioinformatics
IAB is primarily being developed by Greg Caporaso(GitHub/Twitter: @gregcaporaso) in the Caporaso Lab at Northern Arizona University. You can find informatio...2255 days ago
Carefully opt for human reference genome
...d as hg38/GRCh38 human reference genome. if you map reads to GRCh38 or hg38, use the following: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for...1536 days ago
G-compass: a comparative genome browser
G-compass (http://www.h-invitational.jp/g-compass/) is a comparative genome browser. It visualizes evolutionarily conserved genomic regions between human and other 12...2213 days ago
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
...a --contig contigs.fa --genome genome.fa --distanceLow distanceLow --distanceHigh distancehigh --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa [--kMer k --insertVa...2208 days ago
2173 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
...ces from a sequence file. Adds metadata in output for easy plotting. gcp: K-mer GC Processor. Creates a matrix o...mbly, calculates both the read and assembly K-mer coverage along with GC% for each sequence in the ass...1980 days ago
GFinisher: a new strategy to refine and finish bacterial genome assemblies
GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/s...2108 days ago
SimLoRD: A read simulator for third generation sequencing reads
...strands of a provided or randomly generated reference sequence. The reference can be read from a FASTA file or randomly generated with a given GC content. It can consist of se...2081 days ago
LoRMA: A tool for correcting sequencing errors in long reads
...Furthermore, when the coverage of the read set is at least 75×, the throughput of the new method is at least 20% higher. conda install -c atgc-montpellier lorma...2066 days ago