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• • Jit@jit.aber

  

  Jit answered the question [E::bwa_idx_load_from_disk] fail to locate the index files 2906 days ago

  You need to run bwa index  $ bwa index genome.fa[bwa_index] Pack FASTA... 1.64 sec[bwa_index] Construct BWT for the packed sequence...[BWTIncCreate] textLength=235383718, availableWord=28562204[BWTIncConstructFromPacked] 10 iterations done....
• • Aaryan Lokwani@aaryan

  

  Aaryan Lokwani asked [E::bwa_idx_load_from_disk] fail to locate the index files 2906 days ago

  I receive this error while mapping with BWA MEM ! How to fix it ?
• • Jit@jit.aber

  

  Jit bookmarked S-plot2: creates an interactive, two-dimensional heatmap of sequences 2906 days ago

  S-plot2 creates an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2, whole eukaryotic chromosomes and smaller prokaryotic genomes can...

  https://bitbucket.org/lkalesinskas/splot
• • BioStar@biostar

  

  BioStar bookmarked HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome... 2907 days ago

  HM2 can process any diploid assemblies, but it is especially suitable for diploid assemblies with high heterozygosity (≥3%), which can be difficult for other tools. This pipeline also implements flexible and sensitive assembly error detection, a...

  https://github.com/mapleforest/HaploMerger2/releases/
• • BioStar@biostar

  

  BioStar created a new bio-script Perl script to split fasta sequence / overlaps 2908 days ago
• • BioStar@biostar

  

  BioStar posted to the wire 2908 days ago

  Split the fasta $ pyfasta split -k 100 -o 20 input.fasta -n 1 #split #pyfasta #overlaps
• • Shruti Paniwala@shruti

  

  Shruti Paniwala is now a friend with Surender Kumar 2909 days ago

  • Shruti Paniwala@shruti

  

  • Surender Kumar@surenderbioinformatist1980

  
• • Surender Kumar@surenderbioinformatist1980

  

  Surender Kumar is now a friend with Shruti Paniwala 2909 days ago

  • Surender Kumar@surenderbioinformatist1980

  

  • Shruti Paniwala@shruti

  
• • Abhimanyu Singh@abhimanyu

  

  Abhimanyu Singh bookmarked rHAT: a seed-and-extension-based noisy long read alignment tool 2911 days ago

  rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT)...

  https://github.com/dfguan/rHAT
• • Jit@jit.aber

  

  Jit answered the question What are the difference between 3C, 4C and Hi-C methods ? 2911 days ago

  In general intereration point of view, the 3C probe for an interaction between two specific regions that you identify a priori. In 4C, one fragment of interest is known, and you probe for all the potential fragments interacting with your...
• • Rahul Nayak@rahul

  

  Rahul Nayak asked What are the difference between 3C, 4C and Hi-C methods ? 2911 days ago

  3C: chromosome conformation capture 4C:chromosome conformation capture-on-chip 5C : chromosome conformation capture carbon copy
• • Rahul Nayak@rahul

  

  Rahul Nayak posted to the wire 2912 days ago

  Nice genome assembly tutorial http://aidenlab.org/assembly/manual_180322.pdf #Assembly #Tutorial #Genome #NGS
• • BioStar@biostar

  

  BioStar posted to the wire 2912 days ago

  Remove empty line from fasta. $ sed -i '/^$/d' standard_output.final.scaffolds_online.fasta #Empty #Fasta #Remove
• • BioStar@biostar

  

  BioStar posted to the wire 2912 days ago

  MultiLine fasta to oneline fasta converter awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa #Multiline #Oneline
• • BioStar@biostar

  

  BioStar posted to the wire 2913 days ago

  Understanding Paired End and Mate pair reads http://www.biorigami.com/wp-content/uploads/2012/02/PAIREDEND-MATEPAIR.pdf #Reads #Mate #Pairs #PE #Reads #MatePair
• • BioStar@biostar

  

  BioStar bookmarked PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the... 2913 days ago

  Development packages for zlib and libbz2 are needed, as well as a standard compiler environment. On Ubuntu, this can be installed via: sudo apt-get install build-essential libtool automake zlib1g-dev libbz2-dev pkg-config On MacOS, the Apple...

  https://github.com/neufeld/pandaseq
• • Jit@jit.aber

  

  Jit created a new bio-script Generate simulated polyploid genome ! 2913 days ago
• • Jit@jit.aber

  

  Jit bookmarked KAST: Perform Alignment-free k-tuple frequency comparisons from sequences 2914 days ago

  Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.

  https://github.com/martinjvickers/KAST
• • Jit@jit.aber

  

  Jit bookmarked d2Tools: The toolbox for counting the frequency of k-tuple from sequencing datasets and calculate... 2914 days ago

  d2Tools are the toolbox for counting the frequency of K-tuple from sequencing datasets and then calculating the pairwise dissimilarity matrix between samples with the d2-style(d2/d2*/d2S representing d2/d2Star/d2shepp, respectively)...

  https://code.google.com/archive/p/d2-tools/
• • Jit@jit.aber

  

  Jit bookmarked funannotate: Eukaryotic Genome Annotation Pipeline 2915 days ago

  Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes. The impetus for this...

  https://github.com/nextgenusfs/funannotate

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