Jit
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Environmental Genomics Group SciLifeLab/KTH Stockholm
By BioStar 725 days agohttps://github.com/envgen - Useful Metagenomics resourcesLRCstats: Long Read Correction Statistics
By Jit 2515 days agogithub.com - LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation...LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
By Abhimanyu Singh 2271 days agowww.healthcare.uiowa.edu - Added Command line argument support. Multi-stage execution modes. Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N. Better compressed intermediate files. Added...INC-Seq: accurate single molecule reads using nanopore sequencing
By Jit 2554 days agogithub.com - INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling...GenomeMapper: Simultaneous alignment of short reads against multiple genomes
By Jit 2375 days ago1001genomes.org - GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single...SimLoRD: A read simulator for third generation sequencing reads
By Aaryan Lokwani 2286 days agobitbucket.org - SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model. Reads are simulated from both strands of a provided or randomly generated reference sequence. The reference...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 1969 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
By Jit 1750 days agogithub.com - Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep convolutional neural network classifier, using many of the architectural advances that have proven successful in image classification. Unlike...Bioinformatics tools for telomere to telomere assembly !
By BioStar 1195 days agooptimize HiFi readsTrimmomatic: A flexible read trimming tool for Illumina NGS data
By Jit 3145 days agowww.usadellab.org - Paired End: java -jar trimmomatic-0.35.jar PE -phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10...
